Date of Graduation

5-2012

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Cell & Molecular Biology (PhD)

Degree Level

Graduate

Department

Crop, Soil & Environmental Sciences

Advisor

Pengyin Chen

Committee Member

Navam Hettiarachchy

Second Committee Member

Esten Mason

Third Committee Member

Ines Pinto

Keywords

Biological sciences; Molecular markers; Qtl; SSR markers; Seed calcium; Soybean

Abstract

The health benefits and the nutritional values of soyfood products have expanded the demand for food-grade soybean varieties. For whole soyfood products such as natto, small seeded varieties with proper texture are essential. Seed calcium content and hardness are main factors in determining the seed texture. Utilizing molecular markers associated with quantitative trait loci (QTL) for marker assisted selection (MAS) has been an efficient technique for breeders. To find molecular markers associated with a trait is an initial step. The confirmation of QTL in different environments and in different genetic backgrounds is important for MAS. The objectives of this research were to identify SSR markers and QTL associated with seed calcium content and hardness, to confirm previously reported QTL in different genetic backgrounds using mapping populations and advanced breeding lines, and to identify correlation between seed calcium content and hardness. RILs derived from KS4303sp (low calcium/soft-seeded) x PI 407818 B (high calcium/hard-seeded) and PI 407818 B (high calcium) x PI 408052 C (low calcium) were analyzed to identify SSR markers and QTL for seed calcium content and hardness. These RIL populations were grown in a randomized complete block design (RCBD) with two replications, at Fayetteville, AR and Keiser, AR in 2008 and 2009. Interval mapping for the SSR markers revealed a new putative QTL Ca5 for seed calcium content. This QTL is linked to the markers Sat_290 and Satt115 on chromosome 18. In addition, regions on chromosomes 1, 2, 5, 7, 8, 18, and 20 contained environmentally stable markers significantly associated with seed calcium content.

RIL population derived from KS4303sp x PI 407818 B was used to identify SSR markers and QTL associated with seed hardness. Interval mapping for the SSR markers revealed a new putative QTL associated with seed hardness. This QTL is linked to the markers Satt547 and Satt414 on chromosome 16. Single marker analysis also revealed 12 markers associated with seed hardness on 7 different chromosomes of soybean.

One hundred sixty four advanced breeding lines derived from six different crosses with contrasting seed calcium content and hardness and the population derived from KS4303sp x PI 407818 B were used to identify correlation between these two traits. Most of the populations showed positive correlation between seed calcium content and hardness. One hundred sixty four advanced breeding lines from six crosses also were used to confirm previously reported and newly identified QTL for seed calcium content and hardness. Previously reported calcium QTL (Ca1, Ca2, and Ca4) and newly identified QTL (Ca5) were confirmed in these advanced lines. In addition, markers Satt267 and Sat_345 on chromosome 1, Sat_288 on chromosome 7, Sat_228, Satt341, Sat_392 on chromosome 8, Satt547 on chromosome 16, and Satt002 on chromosome 17 were most consistent markers associated with calcium content across populations and environments. Previously reported hardness QTL (Ha1 and Ha2) and newly identified QTL (Ha3) were confirmed in these advanced lines. Moreover, markers Satt267 on chromosome 1, Satt680 on chromosome 7, Satt341 on chromosome 8, and Sct_010 on chromosome 19 were stable across populations and environments for seed hardness. Most consistent markers across populations and environments are the best candidates for MAS. Findings of this research will facilitate MAS for seed calcium content and hardness in soybean breeding programs for food grade soybeans.

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