| Soybean[Glycine max（L）.Merr.]is an important crop used for oil,as well as a major source of edible plant-based protein.Although soybean originated in China,its self-sufficiency rate is relatively low,and more than 85%of soybean consumed in China relies on imports.Therefore,there is a pressing need to increase the production of soybean,with the aim of improving soybean self-sufficiency and ensuring food security.The application of elite cultivars is a hallmark of soybean science and technology development in China,with the key tasks of enhancing selection efficiency and breeding high-yield,high-quality novel cultivars.Current soybean breeding is mainly based on conventional methods,the efficiency of molecular marker-assisted selection for major genes is high,and there is a lack of effective molecular breeding systems for the study of complex traits,such as yield and quality,which are controlled by multiple genes.New high-throughput breeding tools are urgently needed to accelerate the process of genetic research and molecular breeding in soybean.In this study,a high-throughput soybean single nucleotide polymorphism（SNP）array called“Zhongdouxin No.1”（ZDX1）was applied to a breeding population.The array was evaluated for genotyping,elite germplasm selection,breeding criteria establishment,and genomic selection accuracy.The aim was to establish a new breeding system based on a high-throughput functional SNP array that provides a reference for promoting the efficiency of soybean breeding selection and the breeding pipeline of elite cultivars.The key findings are summarized as follows.1.Analysis of phenotypic variation in breeding populationsThe breeding population in this experiment included non-parental lines,parental lines,and their progeny,and the phenotypic variation of the three subpopulations was rich and significant.The distances between non-parental lines all exceeded those of parental and progeny lines,indicating that the non-parental population is potentially useful for soybean breeding.Correlation analysis showed a significant positive correlation between yield and beginning maturity(r MP=0.56).There was a significant negative correlation between protein and oil content(r MP=-0.60).Heritability was>0.9 for beginning maturity and 100-seed weight,0.82 for protein content,0.88 for oil content,and 0.65 for plot yield.2.Population genetic diversity analysis and fixed loci selectionLinkage disequilibrium analysis showed that the r2 decay rate of non-parental lines was greater than that of parental and progeny lines,and the same trend was found for the genetic diversity index.These results indicated that non-parental lines had a higher genetic diversity than parental lines and progeny.A total of 6579 fixed loci（minor allele frequency=0）were selected in progeny,of which 235 had minor allele frequency values greater than 0.01 in both parental and non-parental lines,including 21 nonsynonymous SNPs and two stop-gain SNPs in23 important genes.Loci and gene fixed during breeding may be associated with the selection of important breeding target traits by breeders.3.Selection of elite accessions based on the functional loci of important traitsTen extra-early maturity parents were selected using e1-fs,e1-as,e3-fs,and e4-kes loci in ZDX1,and four early maturity accessions were identified using Mass ARRAY and nine additional loci.Seven cyst nematode-resistant accessions carrying resistance loci rhg1,Rhg4,and SCN3-11 were identified,namely Kangxian1hao,Kangxian5hao,and Kangxian8hao,which were known to be resistant,and Shundou5hao,Qinong1hao,and Fengdou23 and HJ15-863,which were not known to be resistant.The genotype of leaf shape locus Ln was in good agreement with the phenotype,and the proportion of accessions with lanceolate leaflets was70.77%,which was associated with more than four seeds per pod,and it enables greater light transmission through the canopy.4.Breeding criteria based on the breeding index and genetic distanceAnalysis of the phenotypic data of five traits of parental and progeny lines and the genetic distances between parents revealed that a farther genetic distance was associated with a higher probability of heterobeltiosis,and the mean progeny value of the trait was positively correlated with the mid-parent value.The breeding index（BI）was calculated using the weight of the traits,and parents were divided into high,medium,and low subgroups based on the BI.Among the progeny with BI values in the top 10%,73.3%descended from at least one parent with a high BI,and these progeny had greater genetic distances between parents.Therefore,genetically distant parents can be used to broaden the genetic base and help improve the chances of selecting elite progeny.Moreover,12 parents without elite progeny and 21 non-parental lines with short genetic distances from parental lines were eliminated,and 46 high-potential combinations were proposed to further optimize the parent population structure and improve breeding efficiency.5.Accuracy of array-based genomic selectionIn the prediction of five traits,the accuracy of genomic best linear unbiased prediction（GBLUP）based on ZDX1 was significantly higher than pedigree-based best linear unbiased prediction（ABLUP）and combined best linear unbiased prediction（HBLUP）.This indicated that the genomic information provided by the array can better reflect the genetic structure of the breeding population.Analysis of four traits（100-seed weight,protein,oil,and beginning maturity）using the GBLUP model revealed that prediction accuracy was significantly improved using genic region markers that carry more information than whole genomic and intergenic markers.A genome-wide association study showed that,when loci with p<0.1 were used for prediction,markers about 1/10 of the number of original loci could ensure the accuracy of prediction（>0.6）,which significantly reduced the cost of genotyping.Furthermore,a method was established for genomic selection breeding in which the model was established with parents and expanded with progeny,and the prediction accuracy was increased by 32.1%.6.Optimized breeding program based on arrayIn this study,an enhanced molecular breeding strategy was established based on ZDX1 for parental evaluation,allelic combination,and progeny selection.Genotypes can be tested to exclude redundant parental resources prior to the introduction of new parents.Parents with a high BI can be used to improve the selection efficiency of elite progeny.Genetically distant parents can be used to broaden the genetic basis and range of variation in progeny,which effectively increases the probability of producing elite progeny.The integration of theory and practice provides a reference for the application of arrays in improving the efficiency of breeding selection.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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