Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.)
Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.)
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DOI：
10.3389/fpls.2019.01538
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发表时间：
2019-11-26
影响因子：
5.6
通讯作者：
Warkentin, Thomas D.
中科院分区：
文献类型：
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作者：
Gali, Krishna Kishore;Sackville, Alison;Warkentin, Thomas D.
采用全基因组关联研究（GWAS）鉴定了与大田豌豆（Pisum sativum L.）农艺性状（开花日数、成熟日数、株高、种子产量和种子重）、种子形态（形状和酒窝）和种子品质（蛋白质、淀粉和纤维浓度）相关的基因座。来自非洲（埃塞俄比亚）、亚洲（印度）、澳大利亚、欧洲（白俄罗斯、捷克共和国、丹麦、法国、立陶宛、荷兰、俄罗斯、瑞典、乌克兰和英国）和北美（加拿大和美国）23个不同育种项目的135个豌豆品种被用于GWAS。采用基因分型测序法（GBS）进行基因分型。在最小读深为5，次要等位基因频率为0.05的条件下，筛选出16877个高质量snp用于标记-性状关联（MTA）测定。染色体间的LD衰减（LD1/2max,90）在20 ~ 80kb之间变化。种群结构分析将其划分为9个亚种群。2013年至2017年，在捷克的奥洛穆茨、美国北达科他州的法戈以及加拿大萨斯喀彻温省的罗斯恩和萨瑟兰进行了多年、多地点的试验。每个性状至少在5个位置年被表型化。确定了在多个试验中一致的mta。Chr5LG3_566189651和Chr5LG3_572899434株高、Chr2LG1_409403647抗倒伏、Chr1LG6_57305683和Chr1LG6_366513463籽粒产量、Chr1LG6_176606388、Chr2LG1_457185、Chr3LG5_234519042和Chr7LG7_8229439种子淀粉浓度、Chr3LG5_194530376种子蛋白浓度分别在不同地点和年份进行鉴定。本研究确定了与豌豆重要性状相关的SNP标记，这些标记有可能用于标记辅助选择，以实现品种的快速改良。
Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.