Open AccessUltra-dense SNP genetic map construction and identification of SiDt gene controlling the determinate growth habit in Sesamum indicum L.
Author(s) -
Haiyang Zhang,
Hongmei Miao,
Chun Li,
Libin Wei,
Yinghui Duan,
Qin Ma,
Jianyi Kong,
Fangfang Xu,
Shuxian Chang
Publication year - 2016
Publication title -
scientific reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.24
H-Index - 213
ISSN - 2045-2322
DOI - 10.1038/srep31556
Subject(s) - sesamum , biology , genetics , snp , single nucleotide polymorphism , quantitative trait locus , locus (genetics) , genome , genotype , determinacy , gene , horticulture , mathematics , mathematical analysis
Sesame ( Sesamum indicum L.) is an important oilseed crop and has an indeterminate growth habit. Here we resequenced the genomes of the parents and 120 progeny of an F 2 population derived from crossing Yuzhi 11 (indeterminate, Dt ) and Yuzhi DS899 (determinate, dt1 ), and constructed an ultra-dense SNP map for sesame comprised of 3,041 bins including 30,193 SNPs in 13 linkage groups (LGs) with an average marker density of 0.10 cM. Results indicated that the same recessive gene controls the determinacy trait in dt1 and a second determinate line, dt2 (08TP092). The QDt1 locus for the determinacy trait was located in the 18.0 cM–19.2 cM interval of LG8. The target SNP, SiDt 27-1, and the determinacy gene, DS899s00170.023 (named here as SiDt ), were identified in Scaffold 00170 of the Yuzhi 11 reference genome, based on genetic mapping and genomic association analysis. Unlike the G397A SNP change in the dt1 genotype, the SiDt allele in dt2 line was lost from the genome. This example of map-based gene cloning in sesame provides proof-of-concept of the utility of ultra-dense SNP maps for accurate genome research in sesame.