Population Structure and Relatedness for Genome-Wide Association Studies.

The estimation of the population structure and genetic relatedness between individuals within a collection of accessions is important in the formation of core collections for the conservation of genetic resources, uncovering the demographic history of the population under study, as well as for association studies. With the recent development of high-throughput genotyping technologies, several algorithms and methods have been developed and implemented in software to estimate the extent of genetic diversity between individuals. In this chapter, our objective is to describe methods to capture population structure and relatedness in a step-by-step fashion.

A Practical Guide to Using Structural Variants for Genome-Wide Association Studies.

Structural variants (SVs) are known to have large functional impacts on phenotypes of agricultural interest, but they have yet to be routinely used for GWAS. Apart from the difficulty in obtaining high-quality SV genotype data for large populations, one of the main hurdles to using SVs for GWAS lies in formatting of genotype data for use with popular GWAS programs. This protocol describes how typical SV genotype data can be formatted for input to three GWAS programs commonly used by the plant genetics community: TASSEL, GAPIT, and mrMLM.

Genome-wide association identifies several QTLs controlling cysteine and methionine content in soybean seed including some promising candidate genes.

Soybean is an important source of protein, oil and carbohydrates, as well as other beneficial nutrients. A major function of proteins in nutrition is to supply adequate amounts of amino acids. Although they are essential for human nutrition, the sulfur-containing amino acids cysteine (Cys) and methionine (Met) are often limited and the genetic control of their content in soybean seeds is poorly characterized.

Identification of loci controlling mineral element concentration in soybean seeds.

Background: Mineral nutrients play a crucial role in the biochemical and physiological functions of biological systems. The enhancement of seed mineral content via genetic improvement is considered as the most promising and cost-effective approach compared alternative means for meeting the dietary needs. The overall objective of this study was to perform a GWAS of mineral content (Ca, K, P and S) in seeds of a core set of 137 soybean lines that are representative of the diversity of early maturing soybeans cultivated in Canada (maturity groups 000-II).