Pub Date : 2024-06-01Epub Date: 2024-05-24DOI: 10.1002/tpg2.20459
Abdulqader Jighly
{"title":"Pitfalls of multi-species SNP arrays introducing new forms of ascertainment bias.","authors":"Abdulqader Jighly","doi":"10.1002/tpg2.20459","DOIUrl":"10.1002/tpg2.20459","url":null,"abstract":"","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141089135","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 : 2024-06-01Epub Date: 2024-05-19DOI: 10.1002/tpg2.20466
Elisabeth Diatta-Holgate, Ben Bergsma, Mitchell R Tuinstra
Dwarfism is a useful trait in many crop plants because it contributes to improved lodging resistance and harvest index. The mutant allele dw3-ref (dwarf3-reference) of sorghum [Sorghum bicolor (L.) Moench] is characterized by an 882 bp tandem duplication in the fifth exon of the gene that is unstable and reverts to wild-type at a frequency greater than 0.001 in many genetic backgrounds. The goal of this research was to identify stable alleles of dw3 (dwarf3) that could be backcrossed into elite parent lines to improve height stability of the crop. To discover new alleles of dw3, a panel consisting mostly of sorghum conversion lines (SC-lines) was screened by polymerase chain reaction for the 882 bp tandem duplication in the fifth exon of dw3-ref. Sanger sequencing was used to characterize the DNA sequence of this fragment in genotypes that did not contain the 882 bp tandem duplication. Sequence analysis identified three indel mutations, including an 82 bp deletion, a 6 bp duplication, and a 15 bp deletion in this region of the gene. Field trials of the donor genotypes with these new alleles indicated no wild-type revertants of dw3-sd3 (dwarf3-stable dwarf), dw3-sd4, and dw3-sd5. These alleles were backcrossed into Tx430. Field trials of backcross progeny (BC2F4) with the dw3-sd3, dw3-sd4, and dw3-sd5 alleles indicated no revertants. The plant height and flowering time characteristics of the backcross progeny were similar or slightly shorter and earlier than the recurrent parent. These findings demonstrate that dw3-sd3, dw3-sd4, and dw3-sd5 alleles will be useful in breeding for the stable dwarf trait.
矮化在许多作物中都是一个有用的性状,因为它有助于提高抗倒伏能力和收获指数。高粱[Sorghum bicolor (L.) Moench]的突变等位基因 dw3-ref(dwarf3-reference)的特征是该基因第五外显子上有一个 882 bp 的串联重复序列,该序列不稳定,在许多遗传背景中回归野生型的频率大于 0.001。本研究的目标是找出 dw3(矮秆 3)的稳定等位基因,将其回交到优良亲本品系中,以提高作物高度的稳定性。为了发现 dw3 的新等位基因,研究人员通过聚合酶链式反应筛选了一个主要由高粱转化系(SC-lines)组成的面板,以检测 dw3-ref 第五外显子中 882 bp 的串联重复。在不含 882 bp 串联重复片段的基因型中,利用 Sanger 测序法确定了该片段的 DNA 序列特征。序列分析确定了基因该区域的三个滞后突变,包括一个 82 bp 的缺失、一个 6 bp 的重复和一个 15 bp 的缺失。对带有这些新等位基因的供体基因型进行的田间试验表明,dw3-sd3(dwarf3-stable dwarf)、dw3-sd4 和 dw3-sd5没有野生型返祖。这些等位基因被回交到 Tx430 中。对带有 dw3-sd3、dw3-sd4 和 dw3-sd5 等位基因的回交后代(BC2F4)进行的田间试验表明,没有出现返祖现象。回交后代的株高和花期特征与复交亲本相似或稍短,花期也比复交亲本早。这些研究结果表明,dw3-sd3、dw3-sd4 和 dw3-sd5 等位基因将有助于稳定矮生性状的育种。
{"title":"Mutations in the dwarf3 gene confer height stability in sorghum.","authors":"Elisabeth Diatta-Holgate, Ben Bergsma, Mitchell R Tuinstra","doi":"10.1002/tpg2.20466","DOIUrl":"10.1002/tpg2.20466","url":null,"abstract":"<p><p>Dwarfism is a useful trait in many crop plants because it contributes to improved lodging resistance and harvest index. The mutant allele dw<sub>3</sub>-ref (dwarf<sub>3</sub>-reference) of sorghum [Sorghum bicolor (L.) Moench] is characterized by an 882 bp tandem duplication in the fifth exon of the gene that is unstable and reverts to wild-type at a frequency greater than 0.001 in many genetic backgrounds. The goal of this research was to identify stable alleles of dw<sub>3</sub> (dwarf3) that could be backcrossed into elite parent lines to improve height stability of the crop. To discover new alleles of dw<sub>3</sub>, a panel consisting mostly of sorghum conversion lines (SC-lines) was screened by polymerase chain reaction for the 882 bp tandem duplication in the fifth exon of dw<sub>3</sub>-ref. Sanger sequencing was used to characterize the DNA sequence of this fragment in genotypes that did not contain the 882 bp tandem duplication. Sequence analysis identified three indel mutations, including an 82 bp deletion, a 6 bp duplication, and a 15 bp deletion in this region of the gene. Field trials of the donor genotypes with these new alleles indicated no wild-type revertants of dw<sub>3</sub>-sd3 (dwarf<sub>3</sub>-stable dwarf), dw<sub>3</sub>-sd4, and dw<sub>3</sub>-sd5. These alleles were backcrossed into Tx430. Field trials of backcross progeny (BC<sub>2</sub>F<sub>4</sub>) with the dw<sub>3</sub>-sd3, dw<sub>3</sub>-sd4, and dw<sub>3</sub>-sd5 alleles indicated no revertants. The plant height and flowering time characteristics of the backcross progeny were similar or slightly shorter and earlier than the recurrent parent. These findings demonstrate that dw<sub>3</sub>-sd3, dw<sub>3</sub>-sd4, and dw<sub>3</sub>-sd5 alleles will be useful in breeding for the stable dwarf trait.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141066174","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 : 2024-06-01Epub Date: 2024-06-26DOI: 10.1002/tpg2.20471
Ibnou Dieng, Brian Gardunia, Giovanny Covarrubias-Pazaran, Dorcus C Gemenet, Bodo Trognitz, Sam Ofodile, Kayode Fowobaje, Solomon Ntukidem, Trushar Shah, Simon Imoro, Leena Tripathi, Hapson Mushoriwa, Ruth Mbabazi, Stella Salvo, John Derera
Regular measurement of realized genetic gain allows plant breeders to assess and review the effectiveness of their strategies, allocate resources efficiently, and make informed decisions throughout the breeding process. Realized genetic gain estimation requires separating genetic trends from nongenetic trends using the linear mixed model (LMM) on historical multi-environment trial data. The LMM, accounting for the year effect, experimental designs, and heterogeneous residual variances, estimates best linear unbiased estimators of genotypes and regresses them on their years of origin. An illustrative example of estimating realized genetic gain was provided by analyzing historical data on fresh cassava (Manihot esculenta Crantz) yield in West Africa (https://github.com/Biometrics-IITA/Estimating-Realized-Genetic-Gain). This approach can serve as a model applicable to other crops and regions. Modernization of breeding programs is necessary to maximize the rate of genetic gain. This can be achieved by adopting genomics to enable faster breeding, accurate selection, and improved traits through genomic selection and gene editing. Tracking operational costs, establishing robust, digitalized data management and analytics systems, and developing effective varietal selection processes based on customer insights are also crucial for success. Capacity building and collaboration of breeding programs and institutions also play a significant role in accelerating genetic gains.
{"title":"Q&A: Methods for estimating genetic gain in sub-Saharan Africa and achieving improved gains.","authors":"Ibnou Dieng, Brian Gardunia, Giovanny Covarrubias-Pazaran, Dorcus C Gemenet, Bodo Trognitz, Sam Ofodile, Kayode Fowobaje, Solomon Ntukidem, Trushar Shah, Simon Imoro, Leena Tripathi, Hapson Mushoriwa, Ruth Mbabazi, Stella Salvo, John Derera","doi":"10.1002/tpg2.20471","DOIUrl":"10.1002/tpg2.20471","url":null,"abstract":"<p><p>Regular measurement of realized genetic gain allows plant breeders to assess and review the effectiveness of their strategies, allocate resources efficiently, and make informed decisions throughout the breeding process. Realized genetic gain estimation requires separating genetic trends from nongenetic trends using the linear mixed model (LMM) on historical multi-environment trial data. The LMM, accounting for the year effect, experimental designs, and heterogeneous residual variances, estimates best linear unbiased estimators of genotypes and regresses them on their years of origin. An illustrative example of estimating realized genetic gain was provided by analyzing historical data on fresh cassava (Manihot esculenta Crantz) yield in West Africa (https://github.com/Biometrics-IITA/Estimating-Realized-Genetic-Gain). This approach can serve as a model applicable to other crops and regions. Modernization of breeding programs is necessary to maximize the rate of genetic gain. This can be achieved by adopting genomics to enable faster breeding, accurate selection, and improved traits through genomic selection and gene editing. Tracking operational costs, establishing robust, digitalized data management and analytics systems, and developing effective varietal selection processes based on customer insights are also crucial for success. Capacity building and collaboration of breeding programs and institutions also play a significant role in accelerating genetic gains.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460147","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 : 2024-06-01Epub Date: 2024-05-22DOI: 10.1002/tpg2.20462
Patrick Obia Ongom, Christian Fatokun, Abou Togola, Ibnou Dieng, Stella Salvo, Brian Gardunia, Saba Baba Mohammed, Ousmane Boukar
Genetic gain has been proposed as a quantifiable key performance indicator that can be used to monitor breeding programs' effectiveness. The cowpea breeding program at the International Institute of Tropical Agriculture (IITA) has developed and released improved varieties in 70 countries globally. To quantify the genetic changes to grain yield and related traits, we exploited IITA cowpea historical multi-environment trials (METs) advanced yield trial (AYT) data from 2010 to 2022. The genetic gain assessment targeted short duration (SD), medium duration (MD), and late duration (LD) breeding pipelines. A linear mixed model was used to calculate the best linear unbiased estimates (BLUE). Regressed BLUE of grain yield by year of genotype origin depicted realized genetic gain of 22.75 kg/ha/year (2.65%), 7.91 kg/ha/year (0.85%), and 22.82 kg/ha/year (2.51%) for SD, MD, and LD, respectively. No significant gain was realized in 100-seed weight (Hsdwt). We predicted, based on 2022 MET data, that recycling the best genotypes at AYT stage would result in grain yield gain of 37.28 kg/ha/year (SD), 28.00 kg/ha/year (MD), and 34.85 kg/ha/year (LD), and Hsdwt gain of 0.48 g/year (SD), 0.68 g/year (MD), and 0.55 g/year (LD). These results demonstrated a positive genetic gain trend for cowpea, indicating that a yield plateau has not yet been reached and that accelerated gain is expected with the recent integration of genomics in the breeding program. Advances in genomics include the development of the reference genome, genotyping platforms, quantitative trait loci mapping of key traits, and active implementation of molecular breeding.
{"title":"Genetic progress in cowpea [Vigna unguiculata (L.) Walp.] stemming from breeding modernization efforts at the International Institute of Tropical Agriculture.","authors":"Patrick Obia Ongom, Christian Fatokun, Abou Togola, Ibnou Dieng, Stella Salvo, Brian Gardunia, Saba Baba Mohammed, Ousmane Boukar","doi":"10.1002/tpg2.20462","DOIUrl":"10.1002/tpg2.20462","url":null,"abstract":"<p><p>Genetic gain has been proposed as a quantifiable key performance indicator that can be used to monitor breeding programs' effectiveness. The cowpea breeding program at the International Institute of Tropical Agriculture (IITA) has developed and released improved varieties in 70 countries globally. To quantify the genetic changes to grain yield and related traits, we exploited IITA cowpea historical multi-environment trials (METs) advanced yield trial (AYT) data from 2010 to 2022. The genetic gain assessment targeted short duration (SD), medium duration (MD), and late duration (LD) breeding pipelines. A linear mixed model was used to calculate the best linear unbiased estimates (BLUE). Regressed BLUE of grain yield by year of genotype origin depicted realized genetic gain of 22.75 kg/ha/year (2.65%), 7.91 kg/ha/year (0.85%), and 22.82 kg/ha/year (2.51%) for SD, MD, and LD, respectively. No significant gain was realized in 100-seed weight (Hsdwt). We predicted, based on 2022 MET data, that recycling the best genotypes at AYT stage would result in grain yield gain of 37.28 kg/ha/year (SD), 28.00 kg/ha/year (MD), and 34.85 kg/ha/year (LD), and Hsdwt gain of 0.48 g/year (SD), 0.68 g/year (MD), and 0.55 g/year (LD). These results demonstrated a positive genetic gain trend for cowpea, indicating that a yield plateau has not yet been reached and that accelerated gain is expected with the recent integration of genomics in the breeding program. Advances in genomics include the development of the reference genome, genotyping platforms, quantitative trait loci mapping of key traits, and active implementation of molecular breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141082599","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 : 2024-06-01Epub Date: 2024-05-26DOI: 10.1002/tpg2.20461
Kashif Akhtar, Noor Ul Ain, P V Vara Prasad, Misbah Naz, Mehtab Muhammad Aslam, Ivica Djalovic, Muhammad Riaz, Shakeel Ahmad, Rajeev K Varshney, Bing He, Ronghui Wen
Nitrogen (N) as an inorganic macronutrient is inevitable for plant growth, development, and biomass production. Many external factors and stresses, such as acidity, alkalinity, salinity, temperature, oxygen, and rainfall, affect N uptake and metabolism in plants. The uptake of ammonium (NH4+) and nitrate (NO3-) in plants mainly depends on soil properties. Under the sufficient availability of NO3- (>1 mM), low-affinity transport system is activated by gene network NRT1, and under low NO3- availability (<1 mM), high-affinity transport system starts functioning encoded by NRT2 family of genes. Further, under limited N supply due to edaphic and climatic factors, higher expression of the AtNRT2.4 and AtNRT2.5T genes of the NRT2 family occur and are considered as N remobilizing genes. The NH4+ ion is the final form of N assimilated by cells mediated through the key enzymes glutamine synthetase and glutamate synthase. The WRKY1 is a major transcription factor of the N regulation network in plants. However, the transcriptome and metabolite profiles show variations in N assimilation metabolites, including glycine, glutamine, and aspartate, under abiotic stresses. The overexpression of NO3- transporters (OsNRT2.3a and OsNRT1.1b) can significantly improve the biomass and yield of various crops. Altering the expression levels of genes could be a valuable tool to improve N metabolism under the challenging conditions of soil and environment, such as unfavorable temperature, drought, salinity, heavy metals, and nutrient stress.
{"title":"Physiological, molecular, and environmental insights into plant nitrogen uptake, and metabolism under abiotic stresses.","authors":"Kashif Akhtar, Noor Ul Ain, P V Vara Prasad, Misbah Naz, Mehtab Muhammad Aslam, Ivica Djalovic, Muhammad Riaz, Shakeel Ahmad, Rajeev K Varshney, Bing He, Ronghui Wen","doi":"10.1002/tpg2.20461","DOIUrl":"10.1002/tpg2.20461","url":null,"abstract":"<p><p>Nitrogen (N) as an inorganic macronutrient is inevitable for plant growth, development, and biomass production. Many external factors and stresses, such as acidity, alkalinity, salinity, temperature, oxygen, and rainfall, affect N uptake and metabolism in plants. The uptake of ammonium (NH<sub>4</sub> <sup>+</sup>) and nitrate (NO<sub>3</sub> <sup>-</sup>) in plants mainly depends on soil properties. Under the sufficient availability of NO<sub>3</sub> <sup>-</sup> (>1 mM), low-affinity transport system is activated by gene network NRT1, and under low NO<sub>3</sub> <sup>-</sup> availability (<1 mM), high-affinity transport system starts functioning encoded by NRT2 family of genes. Further, under limited N supply due to edaphic and climatic factors, higher expression of the AtNRT2.4 and AtNRT2.5T genes of the NRT2 family occur and are considered as N remobilizing genes. The NH<sub>4</sub> <sup>+</sup> ion is the final form of N assimilated by cells mediated through the key enzymes glutamine synthetase and glutamate synthase. The WRKY1 is a major transcription factor of the N regulation network in plants. However, the transcriptome and metabolite profiles show variations in N assimilation metabolites, including glycine, glutamine, and aspartate, under abiotic stresses. The overexpression of NO<sub>3</sub> <sup>-</sup> transporters (OsNRT2.3a and OsNRT1.1b) can significantly improve the biomass and yield of various crops. Altering the expression levels of genes could be a valuable tool to improve N metabolism under the challenging conditions of soil and environment, such as unfavorable temperature, drought, salinity, heavy metals, and nutrient stress.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141154826","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 : 2024-06-01Epub Date: 2024-06-16DOI: 10.1002/tpg2.20469
Cynthia Idhigu Aghogho, Siraj Ismail Kayondo, Saviour J Y Eleblu, Adenike Ige, Isaac Asante, Samuel K Offei, Elizabeth Parkes, Chiedozie Egesi, Edwige Gaby Nkouaya Mbanjo, Trushar Shah, Peter Kulakow, Ismail Y Rabbi
The starchy storage roots of cassava are commonly processed into a variety of products, including cassava granulated processed products (gari). The commercial value of cassava roots depends on the yield and quality of processed products, directly influencing the acceptance of new varieties by farmers, processors, and consumers. This study aims to estimate genetic advance through phenotypic selection and identify genomic regions associated and candidate genes linked with gari yield and quality. Higher single nucleotide polymorphism (SNP)-based heritability estimates compared to broad-sense heritability estimates were observed for most traits highlighting the influence of genetic factors on observed variation. Using genome-wide association analysis of 188 clones, genotyped using 53,150 genome-wide SNPs, nine SNPs located on seven chromosomes were significantly associated with peel loss, gari yield, color parameters for gari and eba, bulk density, swelling index, and textural properties of eba. Future research will focus on validating and understanding the functions of identified genes and their influence on gari yield and quality traits.
木薯的淀粉贮藏根通常被加工成各种产品,包括木薯颗粒加工产品(gari)。木薯根的商业价值取决于加工产品的产量和质量,直接影响着农民、加工商和消费者对新品种的接受程度。本研究旨在通过表型选择评估遗传进展,并确定与加里产量和质量相关的基因组区域和候选基因。与广义遗传力估计值相比,大多数性状都有较高的基于单核苷酸多态性(SNP)的遗传力估计值,这凸显了遗传因素对观察到的变异的影响。利用 53,150 个全基因组 SNP 对 188 个克隆进行基因分型,通过全基因组关联分析发现,位于 7 条染色体上的 9 个 SNP 与果皮损失、加里产量、加里和埃巴的颜色参数、体积密度、膨胀指数和埃巴的纹理特性有显著关联。未来的研究将侧重于验证和了解已鉴定基因的功能及其对嘎里产量和品质性状的影响。
{"title":"Genome-wide association study for yield and quality of granulated cassava processed product.","authors":"Cynthia Idhigu Aghogho, Siraj Ismail Kayondo, Saviour J Y Eleblu, Adenike Ige, Isaac Asante, Samuel K Offei, Elizabeth Parkes, Chiedozie Egesi, Edwige Gaby Nkouaya Mbanjo, Trushar Shah, Peter Kulakow, Ismail Y Rabbi","doi":"10.1002/tpg2.20469","DOIUrl":"10.1002/tpg2.20469","url":null,"abstract":"<p><p>The starchy storage roots of cassava are commonly processed into a variety of products, including cassava granulated processed products (gari). The commercial value of cassava roots depends on the yield and quality of processed products, directly influencing the acceptance of new varieties by farmers, processors, and consumers. This study aims to estimate genetic advance through phenotypic selection and identify genomic regions associated and candidate genes linked with gari yield and quality. Higher single nucleotide polymorphism (SNP)-based heritability estimates compared to broad-sense heritability estimates were observed for most traits highlighting the influence of genetic factors on observed variation. Using genome-wide association analysis of 188 clones, genotyped using 53,150 genome-wide SNPs, nine SNPs located on seven chromosomes were significantly associated with peel loss, gari yield, color parameters for gari and eba, bulk density, swelling index, and textural properties of eba. Future research will focus on validating and understanding the functions of identified genes and their influence on gari yield and quality traits.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332331","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 : 2024-06-01Epub Date: 2024-03-10DOI: 10.1002/tpg2.20443
Dennis N Katuuramu, Amnon Levi, William P Wechter
Sweet-fleshed watermelon (Citrullus lanatus) is an important vegetable crop of the tropical origin. It is widely grown and consumed around the world for its hydration and nutritional quality values. Low-temperature stress can affect early planting, seedling establishment, and expansion of crop production to new areas. A collection of 122 citron watermelon (Citrullus amarus) accessions were obtained from the USDA's National Plant Germplasm Repository System gene bank in Griffin, GA. The accessions were genotyped using whole genome resequencing to generate single nucleotide polymorphisms (SNPs) molecular markers and screened under cold-stressed and non-stressed control conditions. Four low-temperature stress tolerance related traits including shoot biomass, vine length, maximum quantum efficiency of photosystem II, and chlorophyll content were measured under cold-stressed and non-stressed control treatment conditions. Correlation analysis revealed the presence of positive relationships among traits. Broad-sense heritability for all traits ranged from 0.35 to 0.73, implying the presence of genetic contributions to the observed phenotypic variation. Genomic regions underlying these traits across several citron watermelon chromosomes were identified. Four low-temperature stress tolerance related putative candidate genes co-located with the peak SNPs from genome-wide association study. These genomic regions and marker information could potentially be used in molecular breeding to accelerate genetic improvements for low-temperature stress tolerance in watermelon.
{"title":"Mapping the genetic architecture of low-temperature stress tolerance in citron watermelon.","authors":"Dennis N Katuuramu, Amnon Levi, William P Wechter","doi":"10.1002/tpg2.20443","DOIUrl":"10.1002/tpg2.20443","url":null,"abstract":"<p><p>Sweet-fleshed watermelon (Citrullus lanatus) is an important vegetable crop of the tropical origin. It is widely grown and consumed around the world for its hydration and nutritional quality values. Low-temperature stress can affect early planting, seedling establishment, and expansion of crop production to new areas. A collection of 122 citron watermelon (Citrullus amarus) accessions were obtained from the USDA's National Plant Germplasm Repository System gene bank in Griffin, GA. The accessions were genotyped using whole genome resequencing to generate single nucleotide polymorphisms (SNPs) molecular markers and screened under cold-stressed and non-stressed control conditions. Four low-temperature stress tolerance related traits including shoot biomass, vine length, maximum quantum efficiency of photosystem II, and chlorophyll content were measured under cold-stressed and non-stressed control treatment conditions. Correlation analysis revealed the presence of positive relationships among traits. Broad-sense heritability for all traits ranged from 0.35 to 0.73, implying the presence of genetic contributions to the observed phenotypic variation. Genomic regions underlying these traits across several citron watermelon chromosomes were identified. Four low-temperature stress tolerance related putative candidate genes co-located with the peak SNPs from genome-wide association study. These genomic regions and marker information could potentially be used in molecular breeding to accelerate genetic improvements for low-temperature stress tolerance in watermelon.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140094979","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}
Amanda R Peters Haugrud, Ana Laura Achilli, Raquel Martínez-Peña, Valentyna Klymiuk
Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.
{"title":"Future of durum wheat research and breeding: Insights from early career researchers.","authors":"Amanda R Peters Haugrud, Ana Laura Achilli, Raquel Martínez-Peña, Valentyna Klymiuk","doi":"10.1002/tpg2.20453","DOIUrl":"https://doi.org/10.1002/tpg2.20453","url":null,"abstract":"<p><p>Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960444","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 : 2024-03-01Epub Date: 2023-02-27DOI: 10.1002/tpg2.20301
Hermann G Dallinger, Franziska Löschenberger, Naim Azrak, Christian Ametz, Sebastian Michel, Hermann Bürstmayr
Pre-harvest sprouting (PHS), germination of seeds before harvest, is a major problem in global wheat (Triticum aestivum L.) production, and leads to reduced bread-making quality in affected grain. Breeding for PHS resistance can prevent losses under adverse conditions. Selecting resistant lines in years lacking pre-harvest rain, requires challenging of plants in the field or in the laboratory or using genetic markers. Despite the availability of a wheat reference and pan-genome, linking markers, genes, allelic, and structural variation, a complete understanding of the mechanisms underlying various sources of PHS resistance is still lacking. Therefore, we challenged a population of European wheat varieties and breeding lines with PHS conditions and phenotyped them for PHS traits, grain quality, phenological and agronomic traits to conduct genome-wide association mapping. Furthermore, we compared these marker-trait associations to previously reported PHS loci and evaluated their usefulness for breeding. We found markers associated with PHS on all chromosomes, with strong evidence for novel quantitative trait locus/loci (QTL) on chromosome 1A and 5B. The QTL on chromosome 1A lacks pleiotropic effect, for the QTL on 5B we detected pleiotropic effects on phenology and grain quality. Multiple peaks on chromosome 4A co-located with the major resistance locus Phs-A1, for which two causal genes, TaPM19 and TaMKK3, have been proposed. Mapping markers and genes to the pan-genome and chromosomal alignments provide evidence for structural variation around this major PHS-resistance locus. Although PHS is controlled by many loci distributed across the wheat genome, Phs-A1 on chromosome 4A seems to be the most effective and widely deployed source of resistance, in European wheat varieties.
{"title":"Genome-wide association mapping for pre-harvest sprouting in European winter wheat detects novel resistance QTL, pleiotropic effects, and structural variation in multiple genomes.","authors":"Hermann G Dallinger, Franziska Löschenberger, Naim Azrak, Christian Ametz, Sebastian Michel, Hermann Bürstmayr","doi":"10.1002/tpg2.20301","DOIUrl":"10.1002/tpg2.20301","url":null,"abstract":"<p><p>Pre-harvest sprouting (PHS), germination of seeds before harvest, is a major problem in global wheat (Triticum aestivum L.) production, and leads to reduced bread-making quality in affected grain. Breeding for PHS resistance can prevent losses under adverse conditions. Selecting resistant lines in years lacking pre-harvest rain, requires challenging of plants in the field or in the laboratory or using genetic markers. Despite the availability of a wheat reference and pan-genome, linking markers, genes, allelic, and structural variation, a complete understanding of the mechanisms underlying various sources of PHS resistance is still lacking. Therefore, we challenged a population of European wheat varieties and breeding lines with PHS conditions and phenotyped them for PHS traits, grain quality, phenological and agronomic traits to conduct genome-wide association mapping. Furthermore, we compared these marker-trait associations to previously reported PHS loci and evaluated their usefulness for breeding. We found markers associated with PHS on all chromosomes, with strong evidence for novel quantitative trait locus/loci (QTL) on chromosome 1A and 5B. The QTL on chromosome 1A lacks pleiotropic effect, for the QTL on 5B we detected pleiotropic effects on phenology and grain quality. Multiple peaks on chromosome 4A co-located with the major resistance locus Phs-A1, for which two causal genes, TaPM19 and TaMKK3, have been proposed. Mapping markers and genes to the pan-genome and chromosomal alignments provide evidence for structural variation around this major PHS-resistance locus. Although PHS is controlled by many loci distributed across the wheat genome, Phs-A1 on chromosome 4A seems to be the most effective and widely deployed source of resistance, in European wheat varieties.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10795372","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}