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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #321660

Research Project: Defining the Genetic Diversity and Structure of the Soybean Genome and Applications to Gene Discovery in Soybean, Wheat and Common Bean Germplasm

Location: Soybean Genomics & Improvement Laboratory

Title: Validation of the quantitative trait locus underlying soybean plant height using residual heterozygous lines and near isogenic lines across multi-environments

Author
item YAN, LONG - Hebei Academy Of Agriculture & Forestry
item ZHANG, YUAN-YUAN - Hebei Academy Of Agriculture & Forestry
item Song, Qijian
item CREGAN, PERRY - Retired ARS Employee
item YANG, CHUN-YAN - Hebei Academy Of Agriculture & Forestry
item An, Yong-Qiang - Charles
item WU, CHENGJUN - University Of Arkansas
item CHEN, QIANG - Hebei Academy Of Agriculture & Forestry
item LIU, BING-QIANG - Hebei Academy Of Agriculture & Forestry
item DI, RUI - Hebei Academy Of Agriculture & Forestry
item ZHANG, MENG-CHEN - Hebei Academy Of Agriculture & Forestry

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/28/2016
Publication Date: 1/5/2017
Citation: Yan, L., Zhang, Y., Song, Q., Cregan, P., Yang, C., An, Y., Wu, C., Chen, Q., Liu, B., Di, R., Zhang, M. 2017. Validation of the quantitative trait locus underlying soybean plant height using residual heterozygous lines and near isogenic lines across multi-environments. Euphytica. 213:32. doi:10.1007/s10681-016-1833.

Interpretive Summary: Recombinant inbred lines are conventionally used to position the elements/genes/quantitative trait loci (QTL) controlling plant traits and to estimate the gene effect. Instead, in this research, pairs of near iso-genetic lines were used, these lines were derived from multiple generations of backcrossing and their genetic background was near identical except for the genomic regions controlling the plant height. In addition, the lines derived from several self-pollinated single plant of advanced generation after crossing and only segregated at the genomic region controlling plant height were used to validate and pinpoint the plant height genes. The plant height QTL, qPH_6_1 was evaluated by growing the materials in multiple locations and years. Results showed that the genetic effects of this QTL consistently affected plant height and number of nodes, and could explain 80% of the variation of both traits. However, the effects of the QTL on seed size, seed yield, seed protein concentration and oil concentration varied with locations. The study not only provides a useful method to reduce genetic background noise for mapping QTL and estimating their effects, but also provides soybean breeders useful knowledge of this QTL.

Technical Abstract: Illustrating the consistency of a quantitative trait locus (QTL) and evaluating its genetic effects on other traits across multi-locations is important for breeding selection. However, the consistency of most QTL is unclear due to the interference of other loci segregating in the mapping population. The purpose of this study was to identify and evaluate the genetic architecture of a QTL underlying soybean plant height across multi-locations, using a population in which the “genetic noise” caused by other QTL has been eliminated. The qPH_6_1, underlying plant height, is linked to Satt134 and Satt277. The QTL was positioned on chromosome 6 using a BC2F5 family, which was developed using ‘Jidou 12’ as recurrent parent, and ‘Xinbada 2’ as donor parent. The residual heterozygous lines (RHLs) derived from three BC2F5 plants that segregated at qPH_6_1 were used to validate and pinpoint the QTL. Based on composite interval mapping analysis, the qPH_6_1 explained approximately 80% of the variance for plant height and number of nodes. At the Shijiazhuang and Nanpi locations, the lines containing the allele from ‘Jidou 12’ were taller with a higher number of nodes, than those containing the allele from ‘Xinbada 2’. Furthermore, based on the substitution analysis, the qPH_6_1 locus was positioned in a 3.5 cM interval flanked by Satt365 and Satt100, and co-segregated with Satt557, Satt489, Satt134 and Satt289. The analysis of near-isogenic lines (NILs) also showed that qPH_6_1 had a significant impact on plant height and number of nodes across the other ten locations in two years. A larger genetic effect was observed at locations in north China than locations in south China. The qPH_6_1 could only explain 1.6 - 30.4 % of the phenotypic variation for 100-seed weight, protein content, oil content, and grain yield, and its effects on those traits varied with location.