Pub Date : 2023-08-02DOI: 10.1038/s41437-023-00644-3
Wencai Wang, Xianzhi Zhang, Sònia Garcia, Andrew R. Leitch, Aleš Kovařík
{"title":"Correction: Intragenomic rDNA variation—the product of concerted evolution, mutation, or something in between?","authors":"Wencai Wang, Xianzhi Zhang, Sònia Garcia, Andrew R. Leitch, Aleš Kovařík","doi":"10.1038/s41437-023-00644-3","DOIUrl":"10.1038/s41437-023-00644-3","url":null,"abstract":"","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10490972","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 : 2023-07-31DOI: 10.1038/s41437-023-00639-0
Haena Lee, Pooreum Seo, Salina Teklay, Emily Yuguchi, Elena Dalla Benetta, John H. Werren, Patrick M. Ferree
B chromosomes are non-essential, extra chromosomes that can exhibit transmission-enhancing behaviors, including meiotic drive, mitotic drive, and induction of genome elimination, in plants and animals. A fundamental but poorly understood question is what characteristics allow B chromosomes to exhibit these extraordinary behaviors. The jewel wasp, Nasonia vitripennis, harbors a heterochromatic, paternally transmitted B chromosome known as paternal sex ratio (PSR), which causes complete elimination of the sperm-contributed half of the genome during the first mitotic division of fertilized embryos. This genome elimination event may result from specific, previously observed alterations of the paternal chromatin. Due to the haplo-diploid reproduction of the wasp, genome elimination by PSR causes female-destined embryos to develop as haploid males that transmit PSR. PSR does not undergo self-elimination despite its presence with the paternal chromatin until the elimination event. Here we performed fluorescence microscopic analyses aimed at understanding this unexplained property. Our results show that PSR, like the rest of the genome, participates in the histone-to-protamine transition, arguing that PSR does not avoid this transition to escape self-elimination. In addition, PSR partially escapes the chromatin-altering activity of the intracellular bacterium, Wolbachia, demonstrating that this ability to evade chromatin alteration is not limited to PSR’s own activity. Finally, we observed that the rDNA locus and other unidentified heterochromatic regions of the wasp’s genome also seem to evade chromatin disruption by PSR, suggesting that PSR’s genome-eliminating activity does not affect heterochromatin. Thus, PSR may target an aspect of euchromatin to cause genome elimination.
B 染色体是一种非必要的额外染色体，在植物和动物中可以表现出增强传递的行为，包括减数分裂驱动、有丝分裂驱动和诱导基因组淘汰。一个基本但鲜为人知的问题是，是什么特征使 B 染色体表现出这些非凡的行为。宝石蜂（Nasonia vitripennis）体内有一条异色的、由父亲传播的 B 染色体，即父性比（PSR），它能在受精胚胎第一次有丝分裂过程中导致精子贡献的一半基因组被完全消除。这种基因组消除事件可能是由先前观察到的父系染色质的特定改变造成的。由于黄蜂的繁殖方式是单倍体-二倍体，PSR 的基因组消除会导致雌性胚胎发育成传播 PSR 的单倍体雄性胚胎。尽管 PSR 存在于父代染色质中，但在消除事件发生之前，PSR 不会发生自我消除。在此，我们进行了荧光显微分析，旨在了解这一无法解释的特性。我们的研究结果表明，PSR 与基因组的其他部分一样，参与了组蛋白到丙酮的转变，这表明 PSR 并不是为了逃避自我淘汰而避免这一转变。此外，PSR 还能部分躲避胞内细菌 Wolbachia 的染色质改变活性，这表明躲避染色质改变的能力并不局限于 PSR 自身的活性。最后，我们观察到，黄蜂基因组中的 rDNA 基因座和其他未确定的异染色质区域似乎也躲过了 PSR 对染色质的破坏，这表明 PSR 的基因组消除活性并不影响异染色质。因此，PSR 可能是针对异染色质的某个方面导致基因组消除。
{"title":"Ability of a selfish B chromosome to evade genome elimination in the jewel wasp, Nasonia vitripennis","authors":"Haena Lee, Pooreum Seo, Salina Teklay, Emily Yuguchi, Elena Dalla Benetta, John H. Werren, Patrick M. Ferree","doi":"10.1038/s41437-023-00639-0","DOIUrl":"10.1038/s41437-023-00639-0","url":null,"abstract":"B chromosomes are non-essential, extra chromosomes that can exhibit transmission-enhancing behaviors, including meiotic drive, mitotic drive, and induction of genome elimination, in plants and animals. A fundamental but poorly understood question is what characteristics allow B chromosomes to exhibit these extraordinary behaviors. The jewel wasp, Nasonia vitripennis, harbors a heterochromatic, paternally transmitted B chromosome known as paternal sex ratio (PSR), which causes complete elimination of the sperm-contributed half of the genome during the first mitotic division of fertilized embryos. This genome elimination event may result from specific, previously observed alterations of the paternal chromatin. Due to the haplo-diploid reproduction of the wasp, genome elimination by PSR causes female-destined embryos to develop as haploid males that transmit PSR. PSR does not undergo self-elimination despite its presence with the paternal chromatin until the elimination event. Here we performed fluorescence microscopic analyses aimed at understanding this unexplained property. Our results show that PSR, like the rest of the genome, participates in the histone-to-protamine transition, arguing that PSR does not avoid this transition to escape self-elimination. In addition, PSR partially escapes the chromatin-altering activity of the intracellular bacterium, Wolbachia, demonstrating that this ability to evade chromatin alteration is not limited to PSR’s own activity. Finally, we observed that the rDNA locus and other unidentified heterochromatic regions of the wasp’s genome also seem to evade chromatin disruption by PSR, suggesting that PSR’s genome-eliminating activity does not affect heterochromatin. Thus, PSR may target an aspect of euchromatin to cause genome elimination.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10218022","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 : 2023-07-29DOI: 10.1038/s41437-023-00641-6
Michael D. Pointer, Lewis G. Spurgin, Matthew J. G. Gage, Mark McMullan, David S. Richardson
Dispersal behaviour is an important aspect of the life-history of animals. However, the genetic architecture of dispersal-related traits is often obscure or unknown, even in well studied species. Tribolium castaneum is a globally significant post-harvest pest and established model organism, yet studies of its dispersal have shown ambiguous results and the genetic basis of this behaviour remains unresolved. We combine experimental evolution and agent-based modelling to investigate the number of loci underlying dispersal in T. castaneum, and whether the trait is sex-linked. Our findings demonstrate rapid evolution of dispersal behaviour under selection. We find no evidence of sex-biases in the dispersal behaviour of the offspring of crosses, supporting an autosomal genetic basis of the trait. Moreover, simulated data approximates experimental data under simulated scenarios where the dispersal trait is controlled by one or few loci, but not many loci. Levels of dispersal in experimentally inbred lines, compared with simulations, indicate that a single locus model is not well supported. Taken together, these lines of evidence support an oligogenic architecture underlying dispersal in Tribolium castaneum. These results have implications for applied pest management and for our understanding of the evolution of dispersal in the coleoptera, the world’s most species-rich order.
{"title":"Genetic architecture of dispersal behaviour in the post-harvest pest and model organism Tribolium castaneum","authors":"Michael D. Pointer, Lewis G. Spurgin, Matthew J. G. Gage, Mark McMullan, David S. Richardson","doi":"10.1038/s41437-023-00641-6","DOIUrl":"10.1038/s41437-023-00641-6","url":null,"abstract":"Dispersal behaviour is an important aspect of the life-history of animals. However, the genetic architecture of dispersal-related traits is often obscure or unknown, even in well studied species. Tribolium castaneum is a globally significant post-harvest pest and established model organism, yet studies of its dispersal have shown ambiguous results and the genetic basis of this behaviour remains unresolved. We combine experimental evolution and agent-based modelling to investigate the number of loci underlying dispersal in T. castaneum, and whether the trait is sex-linked. Our findings demonstrate rapid evolution of dispersal behaviour under selection. We find no evidence of sex-biases in the dispersal behaviour of the offspring of crosses, supporting an autosomal genetic basis of the trait. Moreover, simulated data approximates experimental data under simulated scenarios where the dispersal trait is controlled by one or few loci, but not many loci. Levels of dispersal in experimentally inbred lines, compared with simulations, indicate that a single locus model is not well supported. Taken together, these lines of evidence support an oligogenic architecture underlying dispersal in Tribolium castaneum. These results have implications for applied pest management and for our understanding of the evolution of dispersal in the coleoptera, the world’s most species-rich order.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539327/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10247832","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 : 2023-07-22DOI: 10.1038/s41437-023-00640-7
Xiaoqin Jin, Gang Shi
The characterization of gene–environment interactions (GEIs) can provide detailed insights into the biological mechanisms underlying complex diseases. Despite recent interest in GEIs for rare variants, published GEI tests are underpowered for an extremely small proportion of causal rare variants in a gene or a region. By extending the aggregated Cauchy association test (ACAT), we propose three GEI tests to address this issue: a Cauchy combination GEI test with fixed main effects (CCGEI-F), a Cauchy combination GEI test with random main effects (CCGEI-R), and an omnibus Cauchy combination GEI test (CCGEI-O). ACAT was applied to combine p values of single-variant GEI analyses to obtain CCGEI-F and CCGEI-R and p values of multiple GEI tests were combined in CCGEI-O. Through numerical simulations, for small numbers of causal variants, CCGEI-F, CCGEI-R and CCGEI-O provided approximately 5% higher power than the existing GEI tests INT-FIX and INT-RAN; however, they had slightly higher power than the existing GEI test TOW-GE. For large numbers of causal variants, although CCGEI-F and CCGEI-R exhibited comparable or slightly lower power values than the competing tests, the results were still satisfactory. Among all simulation conditions evaluated, CCGEI-O provided significantly higher power than that of competing GEI tests. We further applied our GEI tests in genome-wide analyses of systolic blood pressure or diastolic blood pressure to detect gene–body mass index (BMI) interactions, using whole-exome sequencing data from UK Biobank. At a suggestive significance level of 1.0 × 10−4, KCNC4, GAR1, FAM120AOS and NT5C3B showed interactions with BMI by our GEI tests.
{"title":"Cauchy combination methods for the detection of gene–environment interactions for rare variants related to quantitative phenotypes","authors":"Xiaoqin Jin, Gang Shi","doi":"10.1038/s41437-023-00640-7","DOIUrl":"10.1038/s41437-023-00640-7","url":null,"abstract":"The characterization of gene–environment interactions (GEIs) can provide detailed insights into the biological mechanisms underlying complex diseases. Despite recent interest in GEIs for rare variants, published GEI tests are underpowered for an extremely small proportion of causal rare variants in a gene or a region. By extending the aggregated Cauchy association test (ACAT), we propose three GEI tests to address this issue: a Cauchy combination GEI test with fixed main effects (CCGEI-F), a Cauchy combination GEI test with random main effects (CCGEI-R), and an omnibus Cauchy combination GEI test (CCGEI-O). ACAT was applied to combine p values of single-variant GEI analyses to obtain CCGEI-F and CCGEI-R and p values of multiple GEI tests were combined in CCGEI-O. Through numerical simulations, for small numbers of causal variants, CCGEI-F, CCGEI-R and CCGEI-O provided approximately 5% higher power than the existing GEI tests INT-FIX and INT-RAN; however, they had slightly higher power than the existing GEI test TOW-GE. For large numbers of causal variants, although CCGEI-F and CCGEI-R exhibited comparable or slightly lower power values than the competing tests, the results were still satisfactory. Among all simulation conditions evaluated, CCGEI-O provided significantly higher power than that of competing GEI tests. We further applied our GEI tests in genome-wide analyses of systolic blood pressure or diastolic blood pressure to detect gene–body mass index (BMI) interactions, using whole-exome sequencing data from UK Biobank. At a suggestive significance level of 1.0 × 10−4, KCNC4, GAR1, FAM120AOS and NT5C3B showed interactions with BMI by our GEI tests.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9850466","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}
Tree form evolution is an important ecological specialization for woody species, but its evolutionary process with adaptation is poorly understood, especially on the microevolutionary scale. Daphniphyllum macropodum comprises two varieties: a tree variety growing in a warm temperate climate with light snowfall and a shrub variety growing in a cool temperate climate with heavy snowfall in Japan. Chloroplast DNA variations and genome-wide single-nucleotide polymorphisms across D. macropodum populations and D. teijsmannii as an outgroup were used to reveal the evolutionary process of the shrub variety. Population genetic analysis indicated that the two varieties diverged but were weakly differentiated. Approximate Bayesian computation analysis supported a scenario that assumed migration between the tree variety and the southern populations of the shrub variety. We found migration between the two varieties where the distributions of the two varieties are in contact, and it is concordant with higher tree height in the southern populations of the shrub variety than the northern populations. The genetic divergence between the two varieties was associated with snowfall. The heavy snowfall climate is considered to have developed since the middle Quaternary in this region. The estimated divergence time between the two varieties suggests that the evolution of the two varieties may be concordant with such paleoclimatic change.
树形进化是木本物种的重要生态特化，但人们对其适应性进化过程了解甚少，尤其是在微进化尺度上。在日本，Daphniphyllum macropodum 包括两个品种：一个是生长在暖温带小雪气候中的乔木品种，另一个是生长在冷温带大雪气候中的灌木品种。研究人员利用叶绿体 DNA 变异和全基因组单核苷酸多态性分析，对大戟科大戟属植物种群和作为外群的棣棠属植物进行了研究，以揭示灌木品种的进化过程。种群遗传分析表明，这两个变种发生了分化，但分化程度较弱。近似贝叶斯计算分析支持在乔木品种和灌木品种的南方种群之间进行迁移的假设。我们发现，在两个品种分布接触的地方，两个品种之间存在迁移，这与灌木品种南方种群的树高高于北方种群是一致的。两个品种之间的遗传差异与降雪量有关。降雪量大的气候被认为是从该地区第四纪中期开始形成的。两个品种之间的估计分化时间表明，两个品种的进化可能与这种古气候变化一致。
{"title":"Genetic differentiation and evolution of broad-leaved evergreen shrub and tree varieties of Daphniphyllum macropodum (Daphniphyllaceae)","authors":"Watanabe Yoichi, Sae Matsuzawa, Ichiro Tamaki, Atsushi J. Nagano, Sang-Hun Oh","doi":"10.1038/s41437-023-00637-2","DOIUrl":"10.1038/s41437-023-00637-2","url":null,"abstract":"Tree form evolution is an important ecological specialization for woody species, but its evolutionary process with adaptation is poorly understood, especially on the microevolutionary scale. Daphniphyllum macropodum comprises two varieties: a tree variety growing in a warm temperate climate with light snowfall and a shrub variety growing in a cool temperate climate with heavy snowfall in Japan. Chloroplast DNA variations and genome-wide single-nucleotide polymorphisms across D. macropodum populations and D. teijsmannii as an outgroup were used to reveal the evolutionary process of the shrub variety. Population genetic analysis indicated that the two varieties diverged but were weakly differentiated. Approximate Bayesian computation analysis supported a scenario that assumed migration between the tree variety and the southern populations of the shrub variety. We found migration between the two varieties where the distributions of the two varieties are in contact, and it is concordant with higher tree height in the southern populations of the shrub variety than the northern populations. The genetic divergence between the two varieties was associated with snowfall. The heavy snowfall climate is considered to have developed since the middle Quaternary in this region. The estimated divergence time between the two varieties suggests that the evolution of the two varieties may be concordant with such paleoclimatic change.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10585110","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 : 2023-07-13DOI: 10.1038/s41437-023-00638-1
Nicky Wybouw, Emma Van Reempts, Jens Zarka, Flore Zélé, Dries Bonte
Maternally transmitted symbionts such as Wolbachia can alter sex allocation in haplodiploid arthropods. By biasing population sex ratios towards females, these changes in sex allocation may facilitate the spread of symbionts. In contrast to symbiont-induced cytoplasmic incompatibility (CI), the mechanisms that underpin sex allocation distortion remain poorly understood. Using a nuclear genotype reference panel of the haplodiploid mite Tetranychus urticae and a single Wolbachia variant that is able to simultaneously induce sex allocation distortion and CI, we unraveled the mechanistic basis of Wolbachia-mediated sex allocation distortion. Host genotype was an important determinant for the strength of sex allocation distortion. We further show that sex allocation distortion by Wolbachia in haplodiploid mites is driven by increasing egg size, hereby promoting egg fertilization. This change in reproductive physiology was also coupled to increased male and female adult size. Our results echo previous work on Cardinium symbionts, suggesting that sex allocation distortion by regulating host investment in egg size is a common strategy among symbionts that infect haplodiploids. To better understand the relevance that sex allocation distortion may have for the spread of Wolbachia in natural haplodiploid populations, we parametrized a model based on generated phenotypic data. Our simulations show that empirically derived levels of sex allocation distortion can be sufficient to remove invasion thresholds, allowing CI to drive the spread of Wolbachia independently of the initial infection frequency. Our findings help elucidate the mechanisms that underlie the widespread occurrence of symbionts in haplodiploid arthropods and the evolution of sex allocation.
沃尔巴克氏体等经由母体传播的共生体可以改变单倍体节肢动物的性别分配。通过使种群性别比例偏向雌性，这些性别分配的变化可能会促进共生体的传播。与共生体诱导的细胞质不相容（CI）相比，人们对性别分配扭曲的机制仍然知之甚少。我们利用单倍体螨虫 Tetranychus urticae 的核基因型参考面板和能够同时诱导性别分配扭曲和 CI 的单一沃尔巴克氏体变体，揭示了沃尔巴克氏体介导的性别分配扭曲的机理基础。宿主基因型是性别分配扭曲强度的重要决定因素。我们进一步发现，在单倍体螨类中，沃尔巴克氏体的性别分配扭曲是通过增加卵的大小来驱动的，从而促进卵的受精。生殖生理的这种变化还与雌雄成体尺寸的增加有关。我们的研究结果与之前关于红心螨共生体的研究结果一致，表明通过调节宿主对卵大小的投资来扭曲性别分配是感染单倍体螨虫的共生体的共同策略。为了更好地理解性别分配扭曲可能与沃尔巴克氏体在自然单倍体种群中传播的相关性，我们根据生成的表型数据对模型进行了参数化。我们的模拟结果表明，根据经验得出的性别分配扭曲水平足以消除入侵阈值，从而使CI能够独立于初始感染频率而驱动沃尔巴克氏体的传播。我们的发现有助于阐明共生体在单倍体节肢动物中的广泛存在以及性别分配进化的机制。
{"title":"Egg provisioning explains the penetrance of symbiont-mediated sex allocation distortion in haplodiploids","authors":"Nicky Wybouw, Emma Van Reempts, Jens Zarka, Flore Zélé, Dries Bonte","doi":"10.1038/s41437-023-00638-1","DOIUrl":"10.1038/s41437-023-00638-1","url":null,"abstract":"Maternally transmitted symbionts such as Wolbachia can alter sex allocation in haplodiploid arthropods. By biasing population sex ratios towards females, these changes in sex allocation may facilitate the spread of symbionts. In contrast to symbiont-induced cytoplasmic incompatibility (CI), the mechanisms that underpin sex allocation distortion remain poorly understood. Using a nuclear genotype reference panel of the haplodiploid mite Tetranychus urticae and a single Wolbachia variant that is able to simultaneously induce sex allocation distortion and CI, we unraveled the mechanistic basis of Wolbachia-mediated sex allocation distortion. Host genotype was an important determinant for the strength of sex allocation distortion. We further show that sex allocation distortion by Wolbachia in haplodiploid mites is driven by increasing egg size, hereby promoting egg fertilization. This change in reproductive physiology was also coupled to increased male and female adult size. Our results echo previous work on Cardinium symbionts, suggesting that sex allocation distortion by regulating host investment in egg size is a common strategy among symbionts that infect haplodiploids. To better understand the relevance that sex allocation distortion may have for the spread of Wolbachia in natural haplodiploid populations, we parametrized a model based on generated phenotypic data. Our simulations show that empirically derived levels of sex allocation distortion can be sufficient to remove invasion thresholds, allowing CI to drive the spread of Wolbachia independently of the initial infection frequency. Our findings help elucidate the mechanisms that underlie the widespread occurrence of symbionts in haplodiploid arthropods and the evolution of sex allocation.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10217483","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 : 2023-07-05DOI: 10.1038/s41437-023-00636-3
Adriano Pereira de Castro, Flávio Breseghello, Isabela Volpi Furtini, Marley Marico Utumi, José Almeida Pereira, Tuong-Vi Cao, Jérôme Bartholomé
One of the main challenges of breeding programs is to identify superior genotypes from a large number of candidates. By gradually increasing the frequency of favorable alleles in the breeding population, recurrent selection improves the population mean for target traits, increasing the chance to identify promising genotypes. In rice, population improvement through recurrent selection has been used very little to date, except in Latin America. At Embrapa (Brazilian Agricultural Research Corporation), the upland rice breeding program is conducted in two phases: population improvement followed by product development. In this study, the CNA6 population, evaluated over five cycles (3 to 7) of selection, including 20 field trials, was used to assess the realized genetic gain. A high rate of genetic gain was observed for grain yield, at 215 kg.ha−1 per cycle or 67.8 kg.ha−1 per year (3.08%). The CNA6 population outperformed the controls only for the last cycle, with a yield difference of 1128 kg.ha−1. An analysis of the product development pipeline, based on 29 advanced yield trials with lines derived from cycles 3 to 6, showed that lines derived from the CNA6 population had high grain yield, but did not outperform the controls. These results demonstrate that the application of recurrent selection to a breeding population with sufficient genetic variability can result in significant genetic gains for quantitative traits, such as grain yield. The integration of this strategy into a two-phase breeding program also makes it possible to increase quantitative traits while selecting for other traits of interest.
{"title":"Population improvement via recurrent selection drives genetic gain in upland rice breeding","authors":"Adriano Pereira de Castro, Flávio Breseghello, Isabela Volpi Furtini, Marley Marico Utumi, José Almeida Pereira, Tuong-Vi Cao, Jérôme Bartholomé","doi":"10.1038/s41437-023-00636-3","DOIUrl":"10.1038/s41437-023-00636-3","url":null,"abstract":"One of the main challenges of breeding programs is to identify superior genotypes from a large number of candidates. By gradually increasing the frequency of favorable alleles in the breeding population, recurrent selection improves the population mean for target traits, increasing the chance to identify promising genotypes. In rice, population improvement through recurrent selection has been used very little to date, except in Latin America. At Embrapa (Brazilian Agricultural Research Corporation), the upland rice breeding program is conducted in two phases: population improvement followed by product development. In this study, the CNA6 population, evaluated over five cycles (3 to 7) of selection, including 20 field trials, was used to assess the realized genetic gain. A high rate of genetic gain was observed for grain yield, at 215 kg.ha−1 per cycle or 67.8 kg.ha−1 per year (3.08%). The CNA6 population outperformed the controls only for the last cycle, with a yield difference of 1128 kg.ha−1. An analysis of the product development pipeline, based on 29 advanced yield trials with lines derived from cycles 3 to 6, showed that lines derived from the CNA6 population had high grain yield, but did not outperform the controls. These results demonstrate that the application of recurrent selection to a breeding population with sufficient genetic variability can result in significant genetic gains for quantitative traits, such as grain yield. The integration of this strategy into a two-phase breeding program also makes it possible to increase quantitative traits while selecting for other traits of interest.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10272551","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 : 2023-07-04DOI: 10.1038/s41437-023-00634-5
Wencai Wang, Xianzhi Zhang, Sònia Garcia, Andrew R. Leitch, Aleš Kovařík
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
{"title":"Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?","authors":"Wencai Wang, Xianzhi Zhang, Sònia Garcia, Andrew R. Leitch, Aleš Kovařík","doi":"10.1038/s41437-023-00634-5","DOIUrl":"10.1038/s41437-023-00634-5","url":null,"abstract":"The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10584597","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 : 2023-07-03DOI: 10.1038/s41437-023-00635-4
Maximilian Hirschfeld, Adam Barnett, Marcus Sheaves, Christine Dudgeon
Oceanic islands play a central role in the study of evolution and island biogeography. The Galapagos Islands are one of the most studied oceanic archipelagos but research has almost exclusively focused on terrestrial organisms compared to marine species. Here we used the Galapagos bullhead shark (Heterodontus quoyi) and single nucleotide polymorphisms (SNPs) to examine evolutionary processes and their consequences for genetic divergence and island biogeography in a shallow-water marine species without larval dispersal. The sequential separation of individual islands from a central island cluster gradually established different ocean depths between islands that pose barriers to dispersal in H. quoyi. Isolation by resistance analysis suggested that ocean bathymetry and historical sea level fluctuations modified genetic connectivity. These processes resulted in at least three genetic clusters that exhibit low genetic diversity and effective population sizes that scale with island size and the level of geographic isolation. Our results exemplify that island formation and climatic cycles shape genetic divergence and biogeography of coastal marine organisms with limited dispersal comparable to terrestrial taxa. Because similar scenarios exist in oceanic islands around the globe our research provides a new perspective on marine evolution and biogeography with implications for the conservation of island biodiversity.
海洋岛屿在进化和岛屿生物地理学研究中发挥着核心作用。加拉帕戈斯群岛是研究最多的海洋群岛之一，但与海洋物种相比，研究几乎都集中在陆地生物上。在这里，我们利用加拉帕戈斯牛头鲨（Heterodontus quoyi）和单核苷酸多态性（SNPs）来研究一个没有幼虫扩散的浅水海洋物种的进化过程及其对遗传分化和岛屿生物地理学的影响。单个岛屿从中心岛屿群中依次分离出来，逐渐形成了岛屿之间不同的海洋深度，这对 H. quoyi 的扩散构成了障碍。通过阻力分析进行的隔离表明，海洋水深和历史上的海平面波动改变了遗传连接。这些过程至少形成了三个遗传集群，它们的遗传多样性较低，有效种群大小随岛屿大小和地理隔离程度而变化。我们的研究结果说明，岛屿的形成和气候周期决定了沿岸海洋生物的遗传分化和生物地理学，其扩散范围有限，与陆生类群相当。我们的研究为海洋进化和生物地理学提供了一个新的视角，对保护岛屿生物多样性具有重要意义。
{"title":"What Darwin could not see: island formation and historical sea levels shape genetic divergence and island biogeography in a coastal marine species","authors":"Maximilian Hirschfeld, Adam Barnett, Marcus Sheaves, Christine Dudgeon","doi":"10.1038/s41437-023-00635-4","DOIUrl":"10.1038/s41437-023-00635-4","url":null,"abstract":"Oceanic islands play a central role in the study of evolution and island biogeography. The Galapagos Islands are one of the most studied oceanic archipelagos but research has almost exclusively focused on terrestrial organisms compared to marine species. Here we used the Galapagos bullhead shark (Heterodontus quoyi) and single nucleotide polymorphisms (SNPs) to examine evolutionary processes and their consequences for genetic divergence and island biogeography in a shallow-water marine species without larval dispersal. The sequential separation of individual islands from a central island cluster gradually established different ocean depths between islands that pose barriers to dispersal in H. quoyi. Isolation by resistance analysis suggested that ocean bathymetry and historical sea level fluctuations modified genetic connectivity. These processes resulted in at least three genetic clusters that exhibit low genetic diversity and effective population sizes that scale with island size and the level of geographic isolation. Our results exemplify that island formation and climatic cycles shape genetic divergence and biogeography of coastal marine organisms with limited dispersal comparable to terrestrial taxa. Because similar scenarios exist in oceanic islands around the globe our research provides a new perspective on marine evolution and biogeography with implications for the conservation of island biodiversity.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462691/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10215424","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 : 2023-06-23DOI: 10.1038/s41437-023-00631-8
Risa L. Iwasaki, Yoko Satta
Selection on standing genetic variation is important for rapid local genetic adaptation when the environment changes. We report that, for the prostate stem cell antigen (PSCA) gene, different populations have different target haplotypes, even though haplotypes are shared among populations. The C-C-A haplotype, whereby the first C is located at rs2294008 of PSCA and is a low risk allele for gastric cancer, has become a target of positive selection in Asia. Conversely, the C-A-G haplotype carrying the same C allele has become a selection target mainly in Africa. However, Asian and African share both haplotypes, consistent with the haplotype divergence time (170 kya) prior to the out-of-Africa dispersal. The frequency of C-C-A/C-A-G is 0.344/0.278 in Asia and 0.209/0.416 in Africa. Two-dimensional site frequency spectrum analysis revealed that the extent of intra-allelic variability of the target haplotype is extremely small in each local population, suggesting that C-C-A or C-A-G is under ongoing hard sweeps in local populations. From the time to the most recent common ancestor (TMRCA) of selected haplotypes, the onset times of positive selection were recent (3–55 kya), concurrently with population subdivision from a common ancestor. Additionally, estimated selection coefficients from ABC analysis were up to ~3%, similar to those at other loci under recent positive selection. Phylogeny of local populations and TMRCA of selected haplotypes revealed that spatial and temporal switching of positive selection targets is a unique and novel feature of ongoing selection at PSCA. This switching may reflect the potential of rapid adaptability to distinct environments.
{"title":"Spatial and temporal diversity of positive selection on shared haplotypes at the PSCA locus among worldwide human populations","authors":"Risa L. Iwasaki, Yoko Satta","doi":"10.1038/s41437-023-00631-8","DOIUrl":"10.1038/s41437-023-00631-8","url":null,"abstract":"Selection on standing genetic variation is important for rapid local genetic adaptation when the environment changes. We report that, for the prostate stem cell antigen (PSCA) gene, different populations have different target haplotypes, even though haplotypes are shared among populations. The C-C-A haplotype, whereby the first C is located at rs2294008 of PSCA and is a low risk allele for gastric cancer, has become a target of positive selection in Asia. Conversely, the C-A-G haplotype carrying the same C allele has become a selection target mainly in Africa. However, Asian and African share both haplotypes, consistent with the haplotype divergence time (170 kya) prior to the out-of-Africa dispersal. The frequency of C-C-A/C-A-G is 0.344/0.278 in Asia and 0.209/0.416 in Africa. Two-dimensional site frequency spectrum analysis revealed that the extent of intra-allelic variability of the target haplotype is extremely small in each local population, suggesting that C-C-A or C-A-G is under ongoing hard sweeps in local populations. From the time to the most recent common ancestor (TMRCA) of selected haplotypes, the onset times of positive selection were recent (3–55 kya), concurrently with population subdivision from a common ancestor. Additionally, estimated selection coefficients from ABC analysis were up to ~3%, similar to those at other loci under recent positive selection. Phylogeny of local populations and TMRCA of selected haplotypes revealed that spatial and temporal switching of positive selection targets is a unique and novel feature of ongoing selection at PSCA. This switching may reflect the potential of rapid adaptability to distinct environments.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9892594","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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