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

Abstract

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.

Identification of Genomic Regions Associated with Vine Growth and Plant Height of Soybean

“…The selection criteria for the erect RIZN38 plants were winding number = 0 and PH < 10 cm, while the selection criteria for the vining RIZN38 plants were winding number < 10 and PH < 40 cm. These bulks and the 50 individuals used to establish the VB1 and EB1 bulks, as well as the three parental lines, were genotyped using the ‘Zhongdouxin No.1′ (ZDX1) BeadChip, with 159,072 SNPs processed through the Illumina iScan platform (Illumina, Inc., San Diego, CA, USA) [ 45 ]. The SNP alleles were called using the GenomeStudio v2.0.5 Genotyping software (V2011.1, Illumina, Inc., San Diego, CA, USA).…”

Genetic diversity in early maturity Chinese and European elite soybeans: A comparative analysis

“…Genotyping was carried out by the BeadChip with 159,072 SNP markers selected from the No. 1 Zhongdouxin Soybean Breeding Array ZDX1 (Sun et al 2022) by COMPASS BIOTECH-NOLOGY (Beijing Compass Biotechnology Co, Ltd., Beijing, China) through the Illumina iScan platform (Illumina, Inc., San Diego, CA, USA) following a protocol described in Infinium HD Assay Super Manual. The SNP alleles were called using the Genome-Studio genotyping software (V2011.1, Illumina, Inc.).…”

Genetic diversity in early maturity Chinese and European elite soybeans: A comparative analysis

“…Genotyping was carried out by the BeadChip with 159072 SNP markers selected from the No. 1 Zhongdouxin Soybean Breeding Array ZDX1 (Sun et al 2022) by COMPASS BIOTECHNOLOGY (Beijing Compass Biotechnology Co, Ltd., Beijing, China) through the Illumina iScan platform (Illumina, Inc., San Diego, CA, USA) following a protocol described in In nium HD Assay Super Manual. The SNP alleles were called using the GenomeStudio genotyping software (V2011.1, Illumina, Inc.).…”