Agronomic and Molecular Analysis of Populations Developed from a Single Cross of Adapted x Wild Soybean

DELHEIMER, JACOB CHARLES. Agronomic and Molecular Analysis of Populations Developed from a Single Cross of Adapted x Wild Soybean. (Under the direction of Dr. Thomas E. Carter, Jr.). An underutilized source of allelic diversity in cultivated soybean ([Glycine max (L.) Merr. ] is the progenitor species wild soybean, G. soja (Sieb. And Zucc.). The underutilization of wild soybean in soybean breeding programs results from the poor agronomic performance of progeny derived from crosses of the wild to the domesticate. Typically, soybean breeders have implemented backcross breeding as a way to overcome the inherent shortcomings of the progeny derived from these crosses. However, backcrossing has typically been viewed as the most conservative approach to cultivar development, and typically little progress is made in improving quantitative traits. The focus of this research has been on the novel application of plant breeding methods to improve soybean through crosses to the wild soybean. Two replicate populations were derived from nearly 1.3 million F3 progeny of a single cross of wild X domesticated soybean. Selection of F3 plants was centered around an erect main stem phenotype, a rare, yet easily identifiable trait found amongst progeny. Nearly 225, F4-derived progeny were evaluated in replicated yield trials from 2008-2010. 50 breeding lines yielded within 75% of the conventional G. max checks. Transgressive segregation for 100 seed weight and seed protein content was observed. Analysis of breeding lines using 558 single nucleotide polymorphism (SNP) markers showed that lines maintained from 20-48% of the G. soja alleles. Patterns of diversity found within these breeding were analyzed by calculating genetic distance using simple matching coefficients (SMC) calculated from the 558 SNP markers. The MDS plot revealed a distinct relationship between the breeding lines and the G. max parent. A further analysis of SMC coefficients revealed an average relationship between breeding lines of 0.63, which is greater than the expected relationship of 0.5 based on pedigree probabilities. Single marker analysis of variance and multiple linear regression revealed three genomic regions were associated with increased seed yield derived from the G. soja parent, as well as four genomic regions that were associated with greater 100 seed weight. Analysis of the breeding lines also revealed that a judiciously selected group of 16 lines was able to capture all of the SNP diversity found in the breeding material. A separate study was conducted using a large population of F2:3 family derived from a cross of domesticated x wild soybean to study the inheritance of erect plant growth in breeding populations. No F2 plant or F2:3 completely exhibited erect plant growth. However, 118 F2:3 families produced at least one F3 plant that exhibited erect plant growth. A follow study on the segregation patterns of F3:4 families showed that one to three genes were still segregating for after selection. Based on these results, it appears that the segregation of plant type can be explained by the segregation of seven, ten, or twelve genes, and the selection within F3 populations is a viable option for developing breeding material. The last study focused on developing near isogenic lines (NILs) to test for any negative associations between morphological traits of G. soja and agronomic performance. No negative associations were detected in yield trials conducted in three locations. These results show that particular traits associated with G.soja such as purple flower color, may not be associated with lower seed yield or negative linkages can be broken. Taken together, the results of these studies show that the use of large population size combined with visual selection of rare upright plants is an efficient strategy for introgressing allelic diversity from G. soja into soybean breeding programs. This method can offer breeders access to genetic diversity at a level previously never thought possible. Agronomic and Molecular Analysis of Populations Developed from a Single Cross of Adapted x Wild Soybean by Jacob Charles Delheimer A dissertation submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy