Rujian Sun, Bincheng Sun, Yu Tian, Shanshan Su, Yong Zhang, 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, Qi Zhang, Rongqi Guo, Shen Chai, Lei Feng, Jun Wang, Huilong Hong, Jiangyuan Xu, Xindong Yao, Jing Wen, Jiqiang Liu, Yinghui Li & Lijuan Qiu

Theoretical and Applied Genetics April 2022; vol. 135 : 1413–1427

Key message

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.

Abstract

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.

See: https://link.springer.com/article/10.1007/s00122-022-04043-w

Figure 4: The relationship between the top 10% of progeny in multiple traits and their parental lines. The blue box in the center is the top 10% of progeny with high breeding index (BI) values. They are arranged in order from high to low from left to right. The BI values are given below the box. The parents of these lines are classified by BI value; the top third of lines with the highest BI values are the high parents; the middle third are the medium parents; and the bottom third are the low parents. The bar graph at the bottom shows the kinship between the parental lines.