Copley TR, Duceppe MO, O'Donoughue LS.

BMC Genomics. 2018 Mar 1;19(1):167. doi: 10.1186/s12864-018-4558-4.

Abstract

BACKGROUND:

To continue to meet the increasing demands of soybean worldwide, it is crucial to identify key genes regulating flowering and maturity to expand the cultivated regions into short season areas. Although four soybean genes have been successfully utilized in early maturity breeding programs, new genes governing maturity are continuously being identified suggesting that there remains as yet undiscovered loci governing agronomic traits of interest. The objective of this study was to identify novel loci and genes involved in a diverse set of early soybean maturity using genome-wide association (GWA) analyses to identify loci governing days to maturity (DTM), flowering (DTF) and pod filling (DTPF), as well as yield and 100 seed weight in Canadian environments. To do so, soybean plant introduction lines varying significantly for maturity, but classified as early varieties, were used. Plants were phenotyped for the five agronomic traits for five site-years and GWA approaches used to identify candidate loci and genes affecting each trait.

RESULTS:

Genotyping using genotyping-by-sequencing and microarray methods identified 67,594 single nucleotide polymorphisms, of which 31,283 had a linkage disequilibrium < 1 and minor allele frequency > 0.05 and were used for GWA analyses. A total of 9, 6, 4, 5 and 2 loci were detected for GWA analyses for DTM, DTF, DTPF, 100 seed weight and yield, respectively. Regions of interest, including a region surrounding the E1 gene for flowering and maturity, and several novel loci, were identified, with several loci having pleiotropic effects. Novel loci affecting maturity were identified on chromosomes five and 13 and reduced maturity by 7.2 and 3.3 days, respectively. Novel loci for maturity and flowering contained genes orthologous to known Arabidopsis flowering genes, while loci affecting yield and 100 seed weight contained genes known to cause dwarfism.

CONCLUSIONS:

This study demonstrated substantial variation in soybean agronomic traits of interest, including maturity and flowering dates as well as yield, and the utility of GWA analyses in identifying novel genetic factors underlying important agronomic traits. The loci and candidate genes identified serve as promising targets for future studies examining the mechanisms underlying the related soybean traits.

See: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4558-4

Figure 2: SNP distributions across the soybean genome (v2) and SNP effects within the population of plant introduction genotypes. a Gene and SNP distributions used for genotyping across the soybean chromosomes. From the outer to inner circle: Soybean chromosomes 1 to 20; gene locations on the positive and negative chromosome strands; and GBS, SoySNP50K microarray and the merged data set SNP locations. b Distribution of SNPs based on genomic region within the merged data set. c Predicted SNP effects based on degree of impact within the merged data set. d Predicted SNP effects based on function class for SNPs located within coding regions within the merged data set.