Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height

Abstract

<p id="C3">In this study, 252 plants and their parents of Fengshou 24 × Tongjiao 83-611 were genotyped by SNP160K DNA-chip. A high-density genetic linkage map with a total length of 3661.46 cM was constructed, composing of 5861 SNP markers. Seven QTLs of plant height were detected by inclusive composite interval mapping (ICIM), and each one explained 2.56%-10.41% of the variation in plant height. <italic>qPH-6-1</italic> had the highest contribution rate of phenotypic variation and dominant effect, explaining 10.41% of plant height variation, and the additive and dominant effects are -1.72 and 18.94, respectively. The contribution rate of <italic>qPH-18-1</italic> was the second, explaining 9.64% of plant height variation, but <italic>qPH-18-1</italic> has the highest additive effect, reaching -12.42. 11 plants with <italic>qPH-6-1</italic> and <italic>qPH-18-1</italic> genotypes <italic>Q6Q6/Q18Q18</italic> were screened in F₂ population with an average plant height of 167.00 cm, and 16 plants with 2-locus genotypes <italic>q6q6/q18q18</italic> were screened out with an average plant height of 91.25 cm. The addition of 23 SNP markers inside and outside the <italic>qPH-18-1</italic> locus interval narrowed the locus interval from 766.97 kb to 66.03 kb, containing eight genes. Combined with gene annotation and relative expression difference analysis, it was hypothesized that <italic>Glyma.18G279800</italic> and <italic>Glyma.18G280200</italic> might be associated with plant height of soybean. This study provides a molecular reference base and genetic basis for the improvement of soybean plant architecture.