Pub Date : 2025-01-16DOI: 10.1038/s41437-024-00743-9
Saulo F. S. Chaves, Filipe M. Ferreira, Getulio C. Ferreira, Salvador A. Gezan, Kaio Olimpio G. Dias
Genetic competition can obscure the true merit of selection candidates, potentially leading to altered genotype rankings and a divergence between expected and actual genetic gains. Despite a wealth of literature on genetic competition in plant and animal breeding, the separation of genetic values into direct genetic effects (DGE, related to a genotype’s merit) and indirect genetic effects (IGE, related to the effects of a genotype’s alleles on its neighbor''s phenotype) in linear mixed models is often overlooked, likely due to the complexity involved. To address this, we introduce gencomp, a new R package designed to simplify the use of (spatial-) genetic competition models in crop and tree breeding routines. gencomp includes functions for constructing the genetic competition matrix, fitting (spatial-) genetic competition models via the variance-component approach, and extracting key results such as variance components, heritabilities, competition classes, and total genetic values. For tree breeding, gencomp also calculates the merit of different clonal mixtures using the estimated DGE and IGE of the selection candidates. In this paper, we first present the theoretical foundation of the methods implemented in the package. We then demonstrate the use of gencomp with two datasets: one simulated from a Eucalyptus spp. trial and a real potato dataset. We used both datasets to demonstrate the influence of genetic competition in variance component estimates, heritabilities and selection. Despite the dependency on ASReml-R, a paid resource, gencomp is a user-friendly tool that can popularize genetic competition models, contributing to more informed decision-making in plant breeding.
{"title":"Incorporating spatial and genetic competition into breeding pipelines with the R package gencomp","authors":"Saulo F. S. Chaves, Filipe M. Ferreira, Getulio C. Ferreira, Salvador A. Gezan, Kaio Olimpio G. Dias","doi":"10.1038/s41437-024-00743-9","DOIUrl":"10.1038/s41437-024-00743-9","url":null,"abstract":"Genetic competition can obscure the true merit of selection candidates, potentially leading to altered genotype rankings and a divergence between expected and actual genetic gains. Despite a wealth of literature on genetic competition in plant and animal breeding, the separation of genetic values into direct genetic effects (DGE, related to a genotype’s merit) and indirect genetic effects (IGE, related to the effects of a genotype’s alleles on its neighbor''s phenotype) in linear mixed models is often overlooked, likely due to the complexity involved. To address this, we introduce gencomp, a new R package designed to simplify the use of (spatial-) genetic competition models in crop and tree breeding routines. gencomp includes functions for constructing the genetic competition matrix, fitting (spatial-) genetic competition models via the variance-component approach, and extracting key results such as variance components, heritabilities, competition classes, and total genetic values. For tree breeding, gencomp also calculates the merit of different clonal mixtures using the estimated DGE and IGE of the selection candidates. In this paper, we first present the theoretical foundation of the methods implemented in the package. We then demonstrate the use of gencomp with two datasets: one simulated from a Eucalyptus spp. trial and a real potato dataset. We used both datasets to demonstrate the influence of genetic competition in variance component estimates, heritabilities and selection. Despite the dependency on ASReml-R, a paid resource, gencomp is a user-friendly tool that can popularize genetic competition models, contributing to more informed decision-making in plant breeding.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 2","pages":"129-141"},"PeriodicalIF":3.1,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00743-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-12DOI: 10.1038/s41437-024-00744-8
Derek A Roff
Female preference exerts selection on male traits. How such preferences affect male traits, how female preferences change and the genetic correlation between male traits and female preference were examined by an experiment in which females were either mated to males they preferred (S lines) or to males chosen at random from the population (R lines). Female preference was predicted to increase the time spent calling by males. Thirteen other song components were measured. Preference for individual traits was greatest for time spent calling(CALL), volume(VOL) and chirp rate(CHIRP) but the major contributors in the multivariate function were CALL and CHIRP, the univariate influence of VOL arising from correlations to these traits. Estimation of β, the standardized selection differential, for CALL resulting from female preference showed that it was under strong direct selection. However, contrary to prediction, CALL did not change over the course of the experiment whereas VOL, CHIRP and other song components did. Simulation of the experiment using the estimated G matrix showed that lack of change in CALL resulted from indirect genetic effects negating direct effects. Changes in song components were largely due to indirect effects. This experiment showed that female preference may exert strong selection on traits but how they respond to such selection will depend greatly upon the G matrix. As predicted, female preference declined in the R lines. The genetic correlations between preference and preferred traits did not decline significantly more in the R lines, suggesting correlations resulted from both linkage disequilibrium and pleiotropy.
雌性偏好会对雄性性状产生选择作用。实验研究了这种偏好如何影响雄性特征、雌性偏好如何变化以及雄性特征与雌性偏好之间的遗传相关性。根据预测，雌性偏好会增加雄性的鸣叫时间。研究还测量了其它13种鸣唱成分。对单个特征的偏爱程度最高的是鸣叫时间（CALL）、音量（VOL）和鸣叫频率（CHIRP），但多元函数中的主要贡献者是CALL和CHIRP，VOL的单变量影响来自与这些特征的相关性。对雌性偏好导致的 CALL 的标准化选择差值 β 的估计表明，CALL 受到了强烈的直接选择。然而，与预测相反的是，CALL 在实验过程中没有发生变化，而 VOL、CHIRP 和其他鸣唱成分却发生了变化。使用估计的 G 矩阵模拟实验表明，CALL 没有变化是由于间接遗传效应抵消了直接效应。鸣唱成分的变化在很大程度上是由间接效应引起的。该实验表明，雌性偏好可能会对性状产生强烈的选择作用，但它们如何对这种选择做出反应在很大程度上取决于 G 矩阵。正如预测的那样，R品系的雌性偏好下降。偏好和偏好性状之间的遗传相关性在R品系中并没有明显下降，这表明相关性是由连锁不平衡和多义性造成的。
{"title":"The evolution of preferred male traits, female preference and the G matrix: \"Toto, I've a feeling we're not in Kansas anymore\".","authors":"Derek A Roff","doi":"10.1038/s41437-024-00744-8","DOIUrl":"https://doi.org/10.1038/s41437-024-00744-8","url":null,"abstract":"<p><p>Female preference exerts selection on male traits. How such preferences affect male traits, how female preferences change and the genetic correlation between male traits and female preference were examined by an experiment in which females were either mated to males they preferred (S lines) or to males chosen at random from the population (R lines). Female preference was predicted to increase the time spent calling by males. Thirteen other song components were measured. Preference for individual traits was greatest for time spent calling(CALL), volume(VOL) and chirp rate(CHIRP) but the major contributors in the multivariate function were CALL and CHIRP, the univariate influence of VOL arising from correlations to these traits. Estimation of β, the standardized selection differential, for CALL resulting from female preference showed that it was under strong direct selection. However, contrary to prediction, CALL did not change over the course of the experiment whereas VOL, CHIRP and other song components did. Simulation of the experiment using the estimated G matrix showed that lack of change in CALL resulted from indirect genetic effects negating direct effects. Changes in song components were largely due to indirect effects. This experiment showed that female preference may exert strong selection on traits but how they respond to such selection will depend greatly upon the G matrix. As predicted, female preference declined in the R lines. The genetic correlations between preference and preferred traits did not decline significantly more in the R lines, suggesting correlations resulted from both linkage disequilibrium and pleiotropy.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142970578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-08DOI: 10.1038/s41437-024-00742-w
Trenton C. Agrelius, Jeffry L. Dudycha
Maternal effects have been shown to play influential roles in many evolutionary and ecological processes. However, understanding how environmental stimuli induce within-generation responses that transverse across generations remains elusive, particularly when attempting to segregate confounding effects from offspring genotypes. This review synthesizes literature regarding resource- and predation-driven maternal effects in the model system Daphnia, detailing how the maternal generation responds to the environmental stimuli and the maternal effects seen in the offspring generation(s). Our goal is to demonstrate the value of Daphnia as a model system by showing how general principles of maternal effects emerge from studies on this system. By integrating the results across different types of biotic drivers of maternal effects, we identified broadly applicable shared characteristics: 1. Many, but not all, maternal effects involve offspring size, influencing resistance to starvation, infection, predation, and toxins. 2. Maternal effects manifest more strongly when the offspring’s environment is poor. 3. Strong within-generation responses are typically associated with strong across-generation responses. 4. The timing of the maternal stress matters and can raise or lower the magnitude of the effect on the offspring’s phenotype. 5. Embryonic exposure effects could be mistaken for maternal effects. We outline questions to prioritize for future research and discuss the possibilities for integration of ecologically relevant studies of maternal effects in natural populations with the molecular mechanisms that make them possible, specifically by addressing genetic variation and incorporating information on epigenetics. These small crustaceans can unravel how and why non-genetic information gets passed to future generations.
{"title":"Maternal effects in the model system Daphnia: the ecological past meets the epigenetic future","authors":"Trenton C. Agrelius, Jeffry L. Dudycha","doi":"10.1038/s41437-024-00742-w","DOIUrl":"10.1038/s41437-024-00742-w","url":null,"abstract":"Maternal effects have been shown to play influential roles in many evolutionary and ecological processes. However, understanding how environmental stimuli induce within-generation responses that transverse across generations remains elusive, particularly when attempting to segregate confounding effects from offspring genotypes. This review synthesizes literature regarding resource- and predation-driven maternal effects in the model system Daphnia, detailing how the maternal generation responds to the environmental stimuli and the maternal effects seen in the offspring generation(s). Our goal is to demonstrate the value of Daphnia as a model system by showing how general principles of maternal effects emerge from studies on this system. By integrating the results across different types of biotic drivers of maternal effects, we identified broadly applicable shared characteristics: 1. Many, but not all, maternal effects involve offspring size, influencing resistance to starvation, infection, predation, and toxins. 2. Maternal effects manifest more strongly when the offspring’s environment is poor. 3. Strong within-generation responses are typically associated with strong across-generation responses. 4. The timing of the maternal stress matters and can raise or lower the magnitude of the effect on the offspring’s phenotype. 5. Embryonic exposure effects could be mistaken for maternal effects. We outline questions to prioritize for future research and discuss the possibilities for integration of ecologically relevant studies of maternal effects in natural populations with the molecular mechanisms that make them possible, specifically by addressing genetic variation and incorporating information on epigenetics. These small crustaceans can unravel how and why non-genetic information gets passed to future generations.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 2","pages":"142-154"},"PeriodicalIF":3.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00742-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142948038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Male-killing is a microbe-induced reproductive manipulation in invertebrates whereby male hosts are eliminated during development. In the tea tortrix moth Homona magnanima, Osugoroshi viruses 1‒3 (OGVs), belonging to Partitiviridae induce male-killing. The infection patterns of OGVs are diverse; however, how the influence of these patterns of host phenotypes remains largely unknown. Using field-collected larvae, we established a OGV1 and OGV3 double-infection line, in addition to a triple-infection line, and examined the dsRNA segments, purified viral proteins, OGV density, and host phenotypes. PCR analysis demonstrated that the triple-infection line lost one dsRNA segment, whereas the double-infection line lost eight segments, including one RNA-dependent RNA polymerase (RdRp) gene. LC-MS analysis revealed three potential structural proteins in the OGVs. Males died at the larval stage in the triple-infection line and at the embryo-larval stage in the double-infection line of OGV1 and OGV3; the RNA load of female parents did not contribute to the developmental stage at which males died. These findings indicate that the pattern of viral infection, rather than viral RNA load transmitted from female parent, controls the stage of development at which male-killing occurs. Furthermore, the duration of the larval stage of the double-infection line was found to be significantly longer than that of the triple-infection line. The shorter duration of the larval stage of the triple-infection line could be advantageous over the double-infection line in maximizing transmission efficiency.
{"title":"Infection pattern of male-killing viruses alters phenotypes in the tea tortrix moth Homona magnanima","authors":"Takumi Takamatsu, Hiroshi Arai, Yoshiyuki Itoh, Takuma Kozono, Chien-Fu Wu, Kentaro Kitaura, Hiromitsu Moriyama, Maki N. Inoue","doi":"10.1038/s41437-024-00741-x","DOIUrl":"10.1038/s41437-024-00741-x","url":null,"abstract":"Male-killing is a microbe-induced reproductive manipulation in invertebrates whereby male hosts are eliminated during development. In the tea tortrix moth Homona magnanima, Osugoroshi viruses 1‒3 (OGVs), belonging to Partitiviridae induce male-killing. The infection patterns of OGVs are diverse; however, how the influence of these patterns of host phenotypes remains largely unknown. Using field-collected larvae, we established a OGV1 and OGV3 double-infection line, in addition to a triple-infection line, and examined the dsRNA segments, purified viral proteins, OGV density, and host phenotypes. PCR analysis demonstrated that the triple-infection line lost one dsRNA segment, whereas the double-infection line lost eight segments, including one RNA-dependent RNA polymerase (RdRp) gene. LC-MS analysis revealed three potential structural proteins in the OGVs. Males died at the larval stage in the triple-infection line and at the embryo-larval stage in the double-infection line of OGV1 and OGV3; the RNA load of female parents did not contribute to the developmental stage at which males died. These findings indicate that the pattern of viral infection, rather than viral RNA load transmitted from female parent, controls the stage of development at which male-killing occurs. Furthermore, the duration of the larval stage of the double-infection line was found to be significantly longer than that of the triple-infection line. The shorter duration of the larval stage of the triple-infection line could be advantageous over the double-infection line in maximizing transmission efficiency.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 2","pages":"120-128"},"PeriodicalIF":3.1,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01DOI: 10.1038/s41437-024-00736-8
Deanne Cummins, Michael S. Johnson, Joseph L. Tomkins, W. Jason Kennington
Anthropogenic environmental changes continue to threaten species globally. For example, translocation of species has caused unintentional hybridisation, which has contributed to species declines. On the other hand, hybridisation can be used to increase the evolutionary potential of species vulnerable to rapid environmental change, although the benefits of mixing genetically divergent lineages do not come without risks to individual fitness and the long-term viability of populations. Here, we use a combination of genome-wide Single Nucleotide Polymorphism (SNP) markers, mitochondrial DNA sequencing and measurements of growth rate to determine the genetic consequences of hybridisation between two congeneric marine gastropods across 27 years (~18 generations). Multigeneration hybridisation resulted from the introduction of the intertidal periwinkle Bembicium vittatum (a direct developer) into the native range of its congener Bembicium auratum (a species with planktotrophic larval dispersal). Despite significant genetic divergence between the species, we found no direct evidence of outbreeding depression in the admixed population. Instead, we found evidence for heterosis, which dissipated over time. After an initial lag, the frequency of introduced B. vittatum alleles declined dramatically in the hybrid population. However, a few B. vittatum alleles (3.18%) increased significantly in frequency against the overall trend, providing evidence of adaptive introgression. In the context of hybridisation as a conservation management tool, our results provide some evidence of the potential benefits that can be gained, and suggest that the costs due to outbreeding depression can be small.
{"title":"Multigenerational hybridisation results in heterosis and facilitates adaptive introgression, with no evidence of outbreeding depression in a pair of marine gastropods","authors":"Deanne Cummins, Michael S. Johnson, Joseph L. Tomkins, W. Jason Kennington","doi":"10.1038/s41437-024-00736-8","DOIUrl":"10.1038/s41437-024-00736-8","url":null,"abstract":"Anthropogenic environmental changes continue to threaten species globally. For example, translocation of species has caused unintentional hybridisation, which has contributed to species declines. On the other hand, hybridisation can be used to increase the evolutionary potential of species vulnerable to rapid environmental change, although the benefits of mixing genetically divergent lineages do not come without risks to individual fitness and the long-term viability of populations. Here, we use a combination of genome-wide Single Nucleotide Polymorphism (SNP) markers, mitochondrial DNA sequencing and measurements of growth rate to determine the genetic consequences of hybridisation between two congeneric marine gastropods across 27 years (~18 generations). Multigeneration hybridisation resulted from the introduction of the intertidal periwinkle Bembicium vittatum (a direct developer) into the native range of its congener Bembicium auratum (a species with planktotrophic larval dispersal). Despite significant genetic divergence between the species, we found no direct evidence of outbreeding depression in the admixed population. Instead, we found evidence for heterosis, which dissipated over time. After an initial lag, the frequency of introduced B. vittatum alleles declined dramatically in the hybrid population. However, a few B. vittatum alleles (3.18%) increased significantly in frequency against the overall trend, providing evidence of adaptive introgression. In the context of hybridisation as a conservation management tool, our results provide some evidence of the potential benefits that can be gained, and suggest that the costs due to outbreeding depression can be small.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 1","pages":"75-85"},"PeriodicalIF":3.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142768556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-30DOI: 10.1038/s41437-024-00738-6
Charles Addo Nyarko, Elvis Katche, Mariana Báez, Zhenling Lv, Annaliese S. Mason
The establishment of successful interspecies hybrids requires restoration of a stable “2n” chromosome complement which can produce viable “n” gametes. This may occur (rarely) via recombination between non-homologous chromosomes, or more commonly is associated with a doubling of parental chromosome number to produce new homologous pairing partners in the hybrid. The production of unreduced “2n” gametes (gametes with the somatic chromosome number) may therefore be evolutionarily useful by serving as a key pathway for the formation of new polyploid hybrids, as might specific mechanisms permitting recombination between non-homologous chromosomes. Here, we investigated chromosome complements and fertility in third generation interspecific hybrids (AABC) resulting from a cross between allopolyploids Brassica juncea (AABB) × B. napus (AACC) followed by self-pollination for two generations. Chromosome numbers ranged from 2n = 48–74 in the experimental population (35 plants), with 9–16 B genome chromosomes and up to 4 copies of A genome chromosomes. Unreduced gamete production leading to a putative genome structure of approximately AAAABBCC was hence predicted to explain the high chromosome numbers observed. Additionally, the estimation of nuclei number in post-meiotic sporads revealed a higher frequency of unreduced gametes (0.04–5.21%) in the third generation AABC interspecific hybrids compared to the parental Brassica juncea (0.07%) and B. napus (0.13%). Our results suggest that unreduced gamete production in the subsequent generations following interspecific hybridization events may play a critical role in restoration of more stable, fertile chromosome complements.
{"title":"A wide range of chromosome numbers result from unreduced gamete production in Brassica juncea × B. napus (AABC) interspecific hybrids","authors":"Charles Addo Nyarko, Elvis Katche, Mariana Báez, Zhenling Lv, Annaliese S. Mason","doi":"10.1038/s41437-024-00738-6","DOIUrl":"10.1038/s41437-024-00738-6","url":null,"abstract":"The establishment of successful interspecies hybrids requires restoration of a stable “2n” chromosome complement which can produce viable “n” gametes. This may occur (rarely) via recombination between non-homologous chromosomes, or more commonly is associated with a doubling of parental chromosome number to produce new homologous pairing partners in the hybrid. The production of unreduced “2n” gametes (gametes with the somatic chromosome number) may therefore be evolutionarily useful by serving as a key pathway for the formation of new polyploid hybrids, as might specific mechanisms permitting recombination between non-homologous chromosomes. Here, we investigated chromosome complements and fertility in third generation interspecific hybrids (AABC) resulting from a cross between allopolyploids Brassica juncea (AABB) × B. napus (AACC) followed by self-pollination for two generations. Chromosome numbers ranged from 2n = 48–74 in the experimental population (35 plants), with 9–16 B genome chromosomes and up to 4 copies of A genome chromosomes. Unreduced gamete production leading to a putative genome structure of approximately AAAABBCC was hence predicted to explain the high chromosome numbers observed. Additionally, the estimation of nuclei number in post-meiotic sporads revealed a higher frequency of unreduced gametes (0.04–5.21%) in the third generation AABC interspecific hybrids compared to the parental Brassica juncea (0.07%) and B. napus (0.13%). Our results suggest that unreduced gamete production in the subsequent generations following interspecific hybridization events may play a critical role in restoration of more stable, fertile chromosome complements.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 2","pages":"98-108"},"PeriodicalIF":3.1,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00738-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142768554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-28DOI: 10.1038/s41437-024-00733-x
Cathrine Kiel Skovbjerg, Pernille Sarup, Ellen Wahlström, Jens Due Jensen, Jihad Orabi, Lotte Olesen, Just Jensen, Ahmed Jahoor, Guillaume Ramstein
Genome-wide association study (GWAS) is a powerful tool for identifying marker-trait associations that can accelerate breeding progress. Yet, its power is typically constrained in newly established breeding programs where large phenotypic and genotypic datasets have not yet accumulated. Expanding the dataset by inclusion of data from well-established breeding programs with many years of phenotyping and genotyping can potentially address this problem. In this study we performed single- and multi-population GWAS on heading date and lodging in four barley breeding populations with varying combinations of row-type and growth habit. Focusing on a recently established 6-rowed winter (6RW) barley population, single-population GWAS hardly resulted in any significant associations. Nevertheless, the combination of the 6RW target population with other populations in multi-population GWAS detected four and five robust candidate quantitative trait loci for heading date and lodging, respectively. Of these, three remained undetected when analysing the combined populations individually. Further, multi-population GWAS detected markers capturing a larger proportion of genetic variance in 6RW. For multi-population GWAS, we compared the findings of a univariate model (MP1) with a multivariate model (MP2). While both models surpassed single-population GWAS in power, MP2 offered a significant advantage by having more realistic assumptions while pointing towards robust marker-trait associations across populations. Additionally, comparisons of GWAS findings for MP2 and single-population GWAS allowed identification of population-specific loci. In conclusion, our study presents a promising approach to kick-start genomics-based breeding in newly established breeding populations.
{"title":"Multi-population GWAS detects robust marker associations in a newly established six-rowed winter barley breeding program","authors":"Cathrine Kiel Skovbjerg, Pernille Sarup, Ellen Wahlström, Jens Due Jensen, Jihad Orabi, Lotte Olesen, Just Jensen, Ahmed Jahoor, Guillaume Ramstein","doi":"10.1038/s41437-024-00733-x","DOIUrl":"10.1038/s41437-024-00733-x","url":null,"abstract":"Genome-wide association study (GWAS) is a powerful tool for identifying marker-trait associations that can accelerate breeding progress. Yet, its power is typically constrained in newly established breeding programs where large phenotypic and genotypic datasets have not yet accumulated. Expanding the dataset by inclusion of data from well-established breeding programs with many years of phenotyping and genotyping can potentially address this problem. In this study we performed single- and multi-population GWAS on heading date and lodging in four barley breeding populations with varying combinations of row-type and growth habit. Focusing on a recently established 6-rowed winter (6RW) barley population, single-population GWAS hardly resulted in any significant associations. Nevertheless, the combination of the 6RW target population with other populations in multi-population GWAS detected four and five robust candidate quantitative trait loci for heading date and lodging, respectively. Of these, three remained undetected when analysing the combined populations individually. Further, multi-population GWAS detected markers capturing a larger proportion of genetic variance in 6RW. For multi-population GWAS, we compared the findings of a univariate model (MP1) with a multivariate model (MP2). While both models surpassed single-population GWAS in power, MP2 offered a significant advantage by having more realistic assumptions while pointing towards robust marker-trait associations across populations. Additionally, comparisons of GWAS findings for MP2 and single-population GWAS allowed identification of population-specific loci. In conclusion, our study presents a promising approach to kick-start genomics-based breeding in newly established breeding populations.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 1","pages":"33-48"},"PeriodicalIF":3.1,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00733-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-28DOI: 10.1038/s41437-024-00737-7
Frank T. Burbrink, Edward A. Myers
Phylogeographically structured lineages are a common outcome of range-wide population genetic studies. In the southeastern United States, disconnection between populations found at the intersection of the southeastern coastal plains of peninsular Florida and the southeastern plains of the adjacent continent is readily apparent among many plants and animals. However, the timing and maintenance of species boundaries between these distinctly different subtropical and temperate regions remains unknown for all organisms studied there. Using genome-scale data, we examine the timing of origins, gene flow, and the movement of genes under selection in unique ecoregions within the North American racers (Coluber constrictor). Isolation-migration models along with tests of genome-wide selection, locus-environment associations, and spatial and genomic clines demonstrate that two unrecognized species are present and are in contact at the boundary of these two ecoregions. We show that selection at several loci associated with unique environments have maintained species boundaries despite constant levels of gene flow between these lineages over thousands of generations. This research provides a new avenue of research to examine speciation processes in poorly studied biodiversity hotspots.
{"title":"The genetic origins of species boundaries at subtropical and temperate ecoregions in the North American racers (Coluber constrictor)","authors":"Frank T. Burbrink, Edward A. Myers","doi":"10.1038/s41437-024-00737-7","DOIUrl":"10.1038/s41437-024-00737-7","url":null,"abstract":"Phylogeographically structured lineages are a common outcome of range-wide population genetic studies. In the southeastern United States, disconnection between populations found at the intersection of the southeastern coastal plains of peninsular Florida and the southeastern plains of the adjacent continent is readily apparent among many plants and animals. However, the timing and maintenance of species boundaries between these distinctly different subtropical and temperate regions remains unknown for all organisms studied there. Using genome-scale data, we examine the timing of origins, gene flow, and the movement of genes under selection in unique ecoregions within the North American racers (Coluber constrictor). Isolation-migration models along with tests of genome-wide selection, locus-environment associations, and spatial and genomic clines demonstrate that two unrecognized species are present and are in contact at the boundary of these two ecoregions. We show that selection at several loci associated with unique environments have maintained species boundaries despite constant levels of gene flow between these lineages over thousands of generations. This research provides a new avenue of research to examine speciation processes in poorly studied biodiversity hotspots.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 2","pages":"87-97"},"PeriodicalIF":3.1,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00737-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-18DOI: 10.1038/s41437-024-00735-9
Rajiv Boscolo Agostini, Maria Teresa Vizzari, Andrea Benazzo, Silvia Ghirotto
Halyomorpha halys is a polyphagous insect pest, which was first found outside its native regions in 1996, and since then it has rapidly spread worldwide causing damage to agriculture. Investigating the genetic diversity among H. halys populations is essential to understand the colonization history out of its native areas. Analyses based on mtDNA indicate multiple invasions from Asia to European and American continents, as well as serial invasions within invaded countries, but the colonization dynamics are still debated. Recently, genome-wide data (ddRAD) have been published to investigate the genomic structure of H. halys, proposing China as a putative source of multiple serial invasion events to Europe and the Americas. In this study we re-analyze published ddRAD sequences from worldwide populations of H. halys to better elucidate the colonization process. We assessed the genetic diversity in native populations identifying genetic differentiation between populations in China. Furthermore, we observed a complex pattern of population structure in the invaded countries, that may have originated from the occurrence of multiple independent colonization waves through time, from sub-populations present in the native range to Europe and the Americas. We tested alternative colonization hypotheses through Approximate Bayesian Computation comparison of demographic scenarios. Our results support multiple waves of migration from East China to invaded territories and the occurrence of European and American bridgehead effects. These results underline the importance of demographic inference through genome-wide data to investigate biological invasions, whose knowledge become fundamental to establish new strategies of management and control of invasive species.
{"title":"Disentangling the worldwide invasion process of Halyomorpha halys through approximate Bayesian computation","authors":"Rajiv Boscolo Agostini, Maria Teresa Vizzari, Andrea Benazzo, Silvia Ghirotto","doi":"10.1038/s41437-024-00735-9","DOIUrl":"10.1038/s41437-024-00735-9","url":null,"abstract":"Halyomorpha halys is a polyphagous insect pest, which was first found outside its native regions in 1996, and since then it has rapidly spread worldwide causing damage to agriculture. Investigating the genetic diversity among H. halys populations is essential to understand the colonization history out of its native areas. Analyses based on mtDNA indicate multiple invasions from Asia to European and American continents, as well as serial invasions within invaded countries, but the colonization dynamics are still debated. Recently, genome-wide data (ddRAD) have been published to investigate the genomic structure of H. halys, proposing China as a putative source of multiple serial invasion events to Europe and the Americas. In this study we re-analyze published ddRAD sequences from worldwide populations of H. halys to better elucidate the colonization process. We assessed the genetic diversity in native populations identifying genetic differentiation between populations in China. Furthermore, we observed a complex pattern of population structure in the invaded countries, that may have originated from the occurrence of multiple independent colonization waves through time, from sub-populations present in the native range to Europe and the Americas. We tested alternative colonization hypotheses through Approximate Bayesian Computation comparison of demographic scenarios. Our results support multiple waves of migration from East China to invaded territories and the occurrence of European and American bridgehead effects. These results underline the importance of demographic inference through genome-wide data to investigate biological invasions, whose knowledge become fundamental to establish new strategies of management and control of invasive species.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 1","pages":"64-74"},"PeriodicalIF":3.1,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-08DOI: 10.1038/s41437-024-00734-w
Gillian P. McHugo, James A. Ward, Said Ismael Ng’ang’a, Laurent A. F. Frantz, Michael Salter-Townshend, Emmeline W. Hill, Grace M. O’Gorman, Kieran G. Meade, Thomas J. Hall, David E. MacHugh
Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, since that time, substantial genomic differences have evolved between the two lineages. During the last two millennia, genetic exchange in Africa has resulted in a complex tapestry of taurine-indicine ancestry, with most cattle populations exhibiting varying levels of admixture. Similarly, there are several Southern European cattle populations that also show evidence for historical gene flow from indicine cattle, the highest levels of which are found in the Central Italian White breeds. Here we use two different software tools (MOSAIC and ELAI) for local ancestry inference (LAI) with genome-wide high- and low-density SNP array data sets in hybrid African and residually admixed Southern European cattle populations and obtained broadly similar results despite critical differences in the two LAI methodologies used. Our analyses identified genomic regions with elevated levels of retained or introgressed ancestry from the African taurine, European taurine, and Asian indicine lineages. Functional enrichment of genes underlying these ancestry peaks highlighted biological processes relating to immunobiology and olfaction, some of which may relate to differing susceptibilities to infectious diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. Notably, for retained African taurine ancestry in admixed trypanotolerant cattle we observed enrichment of genes associated with haemoglobin and oxygen transport. This may reflect positive selection of genomic variants that enhance control of severe anaemia, a debilitating feature of trypanosomiasis disease, which severely constrains cattle agriculture across much of sub-Saharan Africa.
牛（牛磺酸牛）和牛（籼米牛）至少在 15 万年前分化，从那时起，这两个牛系之间的基因组就出现了巨大差异。在过去的两千年中，非洲的基因交流产生了复杂的金牛-籼牛血统，大多数牛群都表现出不同程度的混血。同样，南欧的一些牛群也显示出来自籼牛历史基因流的证据，其中中意白种牛的基因流水平最高。在这里，我们使用了两种不同的软件工具（MOSAIC 和 ELAI），通过全基因组高密度和低密度 SNP 阵列数据集对非洲杂交牛和南欧残留混血牛进行了本地祖先推断（LAI），尽管使用的两种 LAI 方法存在重大差异，但我们还是得到了大致相似的结果。我们的分析确定了非洲金牛、欧洲金牛和亚洲籼牛血统保留或引入祖先水平较高的基因组区域。这些祖先峰基因的功能富集突显了与免疫生物学和嗅觉有关的生物过程，其中一些过程可能与对传染病的不同易感性有关，包括牛结核病、东海岸热和热带牛瘟。值得注意的是，对于混血锥虫病耐受牛中保留的非洲牛血统，我们观察到与血红蛋白和氧运输相关的基因富集。这可能反映了基因组变异的正向选择，这些变异增强了对严重贫血症的控制，而严重贫血症是锥虫病的一个衰弱特征，严重制约了撒哈拉以南非洲大部分地区的养牛业。
{"title":"Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations","authors":"Gillian P. McHugo, James A. Ward, Said Ismael Ng’ang’a, Laurent A. F. Frantz, Michael Salter-Townshend, Emmeline W. Hill, Grace M. O’Gorman, Kieran G. Meade, Thomas J. Hall, David E. MacHugh","doi":"10.1038/s41437-024-00734-w","DOIUrl":"10.1038/s41437-024-00734-w","url":null,"abstract":"Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, since that time, substantial genomic differences have evolved between the two lineages. During the last two millennia, genetic exchange in Africa has resulted in a complex tapestry of taurine-indicine ancestry, with most cattle populations exhibiting varying levels of admixture. Similarly, there are several Southern European cattle populations that also show evidence for historical gene flow from indicine cattle, the highest levels of which are found in the Central Italian White breeds. Here we use two different software tools (MOSAIC and ELAI) for local ancestry inference (LAI) with genome-wide high- and low-density SNP array data sets in hybrid African and residually admixed Southern European cattle populations and obtained broadly similar results despite critical differences in the two LAI methodologies used. Our analyses identified genomic regions with elevated levels of retained or introgressed ancestry from the African taurine, European taurine, and Asian indicine lineages. Functional enrichment of genes underlying these ancestry peaks highlighted biological processes relating to immunobiology and olfaction, some of which may relate to differing susceptibilities to infectious diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. Notably, for retained African taurine ancestry in admixed trypanotolerant cattle we observed enrichment of genes associated with haemoglobin and oxygen transport. This may reflect positive selection of genomic variants that enhance control of severe anaemia, a debilitating feature of trypanosomiasis disease, which severely constrains cattle agriculture across much of sub-Saharan Africa.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 1","pages":"49-63"},"PeriodicalIF":3.1,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142619107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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