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Dissection of the practical soybean breeding pipeline by developing ZDX1, a high-throughput functional array.
Rujian Sun1,2,3, Bincheng Sun3, Yu Tian2
1College of Agriculture, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
Summary
A new high-throughput soybean array (ZDX1) accelerates crop breeding by enabling rapid, accurate genotyping. This functional array identifies desirable traits and improves selection strategies for superior soybean varieties.
Area of Science:
- Plant genetics and breeding
- Genomics
- Agricultural science
Background:
- Soybean breeding requires efficient methods for evaluating parents and progeny.
- Microarray technology offers rapid, accurate, and economical genotyping solutions.
- Developing high-throughput tools is crucial for accelerating crop improvement.
Purpose of the Study:
- To develop the ZDX1 high-throughput functional soybean array for accelerated breeding.
- To genotype a large collection of soybean accessions and identify genetic markers.
- To evaluate the array's utility in identifying desirable traits and optimizing breeding strategies.
Main Methods:
- Developed the ZDX1 array with 158,959 SNPs covering 90.92% of soybean genes.
- Genotyped 817 soybean accessions, including parental lines and their progeny.
- Utilized resequencing data from 2214 soybean accessions for array design.
- Applied breeding index (BI) and genomic best linear unbiased prediction (GBLUP) for progeny selection and trait prediction.
Main Results:
- Identified fixed SNPs in progeny, indicating artificial selection during breeding.
- Discovered novel soybean cyst nematode-resistant progeny and maturity-related sources through functional site analysis.
- The breeding index (BI) effectively predicted superior progeny derived from distantly related parents.
- Genomic best linear unbiased prediction (GBLUP) using genic SNPs achieved the highest prediction accuracy for traits, improved by 32.1% with expanded training populations.
Conclusions:
- The ZDX1 functional array significantly accelerates soybean breeding through accurate evaluation and selection.
- Functional sites and allele combinations efficiently screen for desirable traits like pest resistance and maturity.
- The breeding index (BI) and GBLUP analysis are valuable tools for optimizing soybean breeding pipelines.
- This versatile assay provides crucial information for designing and enhancing breeding programs.
