Developing core marker sets for effective genomic-assisted selection in wheat and barley breeding programs.

IF 2 4区 农林科学 Q2 AGRONOMY Breeding Science Pub Date : 2022-06-01 Epub Date: 2022-06-29 DOI:10.1270/jsbbs.22004
Goro Ishikawa, Hiroaki Sakai, Nobuyuki Mizuno, Elena Solovieva, Tsuyoshi Tanaka, Kazuki Matsubara
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引用次数: 1

Abstract

Wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) are widely cultivated temperate crops. In breeding programs with these crops in Japan, effective genomic-assisted selection was performed by selecting core marker sets from thousands of genome-wide amplicon sequencing markers. The core sets consist of 768 and 960 markers for barley and wheat, respectively. These markers are distributed evenly across the genomes and effectively detect widely distributed polymorphisms in the chromosomes. The core set utility was assessed using 1,032 barley and 1,798 wheat accessions across the country. Minor allele frequency and chromosomal distributions showed that the core sets could effectively capture polymorphisms across the entire genome, indicating that the core sets are applicable to highly-related advanced breeding materials. Using the core sets, we also assessed the trait value predictability. As observed via fivefold cross-validation, the prediction accuracies of six barley traits ranged from 0.56-0.74 and 0.62 on average, and the corresponding values for eight wheat traits ranged from 0.44-0.83 and 0.65 on average. These data indicate that the established core marker sets enable breeding processes to be accelerated in a cost-effective manner and provide a strong foundation for further research on genomic selection in crops.

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开发小麦和大麦育种计划中有效的基因组辅助选择的核心标记集。
小麦(Triticum aestivum L.)和大麦(Hordeum vulgare L.)是广泛种植的温带作物。在日本的这些作物育种项目中,通过从数千个全基因组扩增子测序标记中选择核心标记集,进行了有效的基因组辅助选择。大麦和小麦的核心组分别由768个和960个标记组成。这些标记在整个基因组中均匀分布,可以有效地检测染色体中广泛分布的多态性。核心集效用是用全国1032个大麦和1798个小麦来评估的。较小的等位基因频率和染色体分布表明,该核心集可以有效捕获整个基因组的多态性,表明该核心集适用于高度相关的高级育种材料。利用核心集,我们还评估了特质价值的可预测性。通过5倍交叉验证,6个大麦性状的预测精度平均为0.56 ~ 0.74和0.62,8个小麦性状的预测精度平均为0.44 ~ 0.83和0.65。这些数据表明,已建立的核心标记集能够以经济有效的方式加快育种过程,并为进一步研究作物基因组选择提供坚实的基础。
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来源期刊
Breeding Science
Breeding Science 农林科学-农艺学
CiteScore
4.90
自引率
4.20%
发文量
37
审稿时长
1.5 months
期刊介绍: Breeding Science is published by the Japanese Society of Breeding. Breeding Science publishes research papers, notes and reviews related to breeding. Research Papers are standard original articles. Notes report new cultivars, breeding lines, germplasms, genetic stocks, mapping populations, database, software, and techniques significant and useful for breeding. Reviews summarize recent and historical events related breeding. Manuscripts should be submitted by corresponding author. Corresponding author must have obtained permission from all authors prior to submission. Correspondence, proofs, and charges of excess page and color figures should be handled by the corresponding author.
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