Dissection of the practical soybean breeding pipeline by developing ZDX1, a high-throughput functional array

生物 SNP基因分型 选择(遗传算法) 单核苷酸多态性 遗传学 基因分型 分子育种 植物育种 大豆孢囊线虫 计算生物学 基因 基因型 农学 计算机科学 人工智能
作者
Lijuan Qiu,Bincheng Sun,Yu Tian,Shanshan Su,Zhang Yong,Wanhai Zhang,Jingshun Wang,Ping Yu,Bingfu Guo,Huihui Li,Yanfei Li,Huawei Gao,Yongzhe Gu,Lili Yu,Yansong Ma,Erhu Su,Qiang Li,Xingguo Hu,Qí Zhāng,Rongqi Guo,Shen Chai,Lei Feng,Jun Wang,Huilong Hong,Jiangyuan Xu,Xindong Yao,Jing Wen,Jiqiang Liu,Yinghui Li,Lijuan Qiu
出处
期刊:Theoretical and Applied Genetics [Springer Science+Business Media]
卷期号:135 (4): 1413-1427 被引量:14
标识
DOI:10.1007/s00122-022-04043-w
摘要

We developed the ZDX1 high-throughput functional soybean array for high accuracy evaluation and selection of both parents and progeny, which can greatly accelerate soybean breeding. Microarray technology facilitates rapid, accurate, and economical genotyping. Here, using resequencing data from 2214 representative soybean accessions, we developed the high-throughput functional array ZDX1, containing 158,959 SNPs, covering 90.92% of soybean genes and sites related to important traits. By application of the array, a total of 817 accessions were genotyped, including three subpopulations of candidate parental lines, parental lines and their progeny from practical breeding. The fixed SNPs were identified in progeny, indicating artificial selection during the breeding process. By identifying functional sites of target traits, novel soybean cyst nematode-resistant progeny and maturity-related novel sources were identified by allele combinations, demonstrating that functional sites provide an efficient method for the rapid screening of desirable traits or gene sources. Notably, we found that the breeding index (BI) was a good indicator for progeny selection. Superior progeny were derived from the combination of distantly related parents, with at least one parent having a higher BI. Furthermore, new combinations based on good performance were proposed for further breeding after excluding redundant and closely related parents. Genomic best linear unbiased prediction (GBLUP) analysis was the best analysis method and achieved the highest accuracy in predicting four traits when comparing SNPs in genic regions rather than whole genomic or intergenic SNPs. The prediction accuracy was improved by 32.1% by using progeny to expand the training population. Collectively, a versatile assay demonstrated that the functional ZDX1 array provided efficient information for the design and optimization of a breeding pipeline for accelerated soybean breeding.
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