Fine mapping and candidate gene identification of a soybean seed protein and oil QTL from a wild soybean accession and linkage analysis for whole plant biomass, carbon, nitrogen, and seed composition using a RIL mapping population
Authors:   , Yang Yia 
Published: August 2021

Soybean [Glycine max (L.) Merr] cultivars have low genetic variation due to domestication, founder events, and selection strategies for modern plant breeding. There is a need to introduce genetic diversity into soybean cultivars for long-term improvement of agronomic and seed compositional traits. In both public and private soybean breeding programs, the introgression of wild soybean (Glycine soja Siebold and Zucc.) genes has been utilized to incorporate novel genetic diversity. In our study, 3,015 single F[subscript 4:9] soybean plants were genotyped for nine genotype-by-sequencing markers from a previous genetic mapping study on recombinant inbred lines (La, 2018) to create two residual heterozygotes derived near isogenic lines (RHD-NIL) populations. The first RHD-NIL population was selected for a novel oil quantitative trait loci (QTL) on chromosome 8 and the second RHD-NIL population was selected for a novel protein QTL on chromosome 14. Both novel QTL derived from the wild soybean accession PI 593983. The objective of this research is to validate these QTL, reduce the QTL interval, and fine map the two novel QTL for candidate gene identification. Single marker analysis and linkage analysis was conducted using SoySNP6K BeadChip markers for QTL validation. The chromosome 8 oil QTL was not advanced for fine mapping because the QTL was not validated in a subsequent field and greenhouse study. Whole genome resequencing was leveraged to reduce the QTL from 16.5 Mbp to approximately 4.6 Mbp and to fine map 50 high protein RHD-NIL, which have segregated for the validated chromosome 14 QTL to permit candidate gene identification. A total of 55 potential candidates was identified in a physical interval of 8,059,955 to 12,648,760 bp. Our results provide a better insight of utilizing wild soybean as a source of genetic diversity for soybean cultivar improvement. In addition to the fine mapping and candidate gene identification study, we conducted linkage analysis for a recombinant inbred line (RIL) mapping population for plant biomass content, whole plant carbon content, whole plant nitrogen content, seed oil content, and seed protein content. Soybean seeds require a large amount of nitrogen because of its high protein content. Through a symbiotic association between soil microorganisms and soybean root nodules, soybean is able to fix atmospheric dinitrogen for nitrogen uptake. Plant biomass was collected by bulking five soybean shoot samples per plot from 262 plots in four locations and bulking three soybean shoots samples per plot from 262 plots in one location. Plant materials were dried and weighed for whole plant biomass weight. Whole plant carbon content, whole plant nitrogen content, seed oil content, and seed protein content was analyzed via near infrared spectroscopy. The objective of this study was to examine nitrogen mobilization from a mapping population from the cross PI 361103 (contains high shoot N content and low seed N content) x PI 567572B (contains high seed N content and low shoot N content), identify QTL for plant biomass, whole plant carbon content, whole plant nitrogen content, and seed composition, and study maternal effects of cytoplasmic inheritance of the five traits from the reciprocal parental cross. Linkage analysis was conducted using BARCSoySNP50K markers. We identified six QTL for plant biomass, two QTL for whole plant carbon content, three QTL for whole plant nitrogen content, three QTL for seed oil content, and five QTL for seed protein content, with multiple traits having overlapping QTL intervals. Our results indicate QTL associated with multiple traits demonstrating the potential of pleiotropic effect in our mapping population.