QTL underlying some agronomic traits in barley detected by SNP markers

Jibin Wang; Genlou Sun; Xifeng Ren; Chengdao Li; Lipan Liu; Qifei Wang; Binbin Du; Dongfa Sun

doi:10.1186/s12863-016-0409-y

QTL underlying some agronomic traits in barley detected by SNP markers

BMC Genet. 2016 Jul 7;17(1):103. doi: 10.1186/s12863-016-0409-y.

Authors

Jibin Wang¹, Genlou Sun², Xifeng Ren¹, Chengdao Li³, Lipan Liu¹, Qifei Wang¹, Binbin Du¹, Dongfa Sun^{4

5}

Affiliations

¹ College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
² Biology Department, Saint Mary's University, 923 Robie Street, Halifax, NS, B3H 3C3, Canada.
³ Department of Agriculture & Food/Agricultural Research Western Australia, 3 Baron-Hay Court, South Perth, WA, 6155, Australia.
⁴ College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. sundongfa1@mail.hzau.edu.cn.
⁵ Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, 434025, Hubei, China. sundongfa1@mail.hzau.edu.cn.

Abstract

Background: Increasing the yield of barley (Hordeum vulgare L.) is a main breeding goal in developing barley cultivars. A high density genetic linkage map containing 1894 SNP and 68 SSR markers covering 1375.8 cM was constructed and used for mapping quantitative traits. A late-generation double haploid population (DH) derived from the Huaai 11 × Huadamai 6 cross was used to identify QTLs and QTL × environment interactions for ten traits affecting grain yield including length of main spike (MSL), spikelet number on main spike (SMS), spikelet number per plant (SLP), grain number per plant (GP), grain weight per plant (GWP), grain number per spike (GS), thousand grain weight (TGW), grain weight per spike (GWS), spike density (SPD) and spike number per plant (SP).

Results: In single environment analysis using composite interval mapping (CIM), a total of 221 QTLs underlying the ten traits were detected in five consecutive years (2009-2013). The QTLs detected in each year were 50, 48, 41, 41 and 41 for the year 2009 to 2013. The QTLs associated with these traits were generally clustered on chromosome 2H, 4H and 7H. In multi-environment analysis, a total of 111 significant QTLs including 18 for MSL, 16 for SMS, 15 for SPD, 5 for SP, 4 for SLP, 14 for TGW, 5 for GP, 11 for GS, 8 for GWP, and 15 for GWS were detected in the five years. Most QTLs showed significant QTL × environment interactions (QEI), nine QTLs (qIMSL3-1, qIMSL4-1, qIMSL4-2, qIMSL6-1, qISMS7-1, qISPD2-7, qISPD7-1, qITGW3-1 and qIGWS4-3) were detected with minimal QEI effects and stable in different years. Among 111 QTLs,71 (63.40 %) QTLs were detected in both single and multiple environments.

Conclusions: Three main QTL cluster regions associated with the 10 agronomic traits on chromosome 2H, 4H and 7H were detected. The QTLs for SMS, SLP, GP and GWP were located in the region near Vrs1 on chromosome 2H. The QTLs underlying SMS, SPD and SLP were clustered on chromosome 4H. On the terminal of chromosome 7H, there was a QTL cluster associated with TGW, SPD, GWP and GWS. The information will be useful for marker-assisted selection (MAS) in barley breeding.

Keywords: Agronomic traits; Barley; Grain yield; High density linkage map; Single nucleotide polymorphism.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genetic Markers / genetics*
Hordeum / anatomy & histology
Hordeum / genetics*
Hordeum / growth & development*
Microsatellite Repeats / genetics
Polymorphism, Single Nucleotide / genetics*
Quantitative Trait Loci / genetics*

Substances

Genetic Markers