QTL underlying some agronomic traits in barley detected by SNP markers

Abstract

BackgroundIncreasing 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).ResultsIn 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.ConclusionsThree 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0409-y) contains supplementary material, which is available to authorized users.

QTL analysis in Barley Across Environments in Egypt

“…RFLP (Kandemir et al 2000) SSR (Li et al, 2006) to map quantitative trait loci (QTLs) in an advanced backcross population of barley, DArT marker (Tondelli et al, 2014) to study the QTLs responsible for barley yield adaptation to the Mediterranean environments. Some studies used two type of markers i.e., RFLP and SSR (Wang, et al 2014) , SNP and SSR markers (Wang et al, 2016) to identify QTLs and QTL × environment interactions for ten grain yield-related traits in a late-generation double haploid population (DH) derived from the Huaai 11 × Huadamai 6 cross . Cuesta-Marcos et al (2008) used 215 markers: 10 RFLP, 5 STS, 5 15 RAPD, 112 AFLP and 73 SSR (15 ESTs and 58 genomic-derived markers, to discover grain yield QTL in a doubled haploid 25 population of barley that is highly productive under the inland plains of Spain.…”

Modelling of genotype by environment interaction and prediction of complex traits across multiple environments as a synthesis of crop growth modelling, genetics and statistics

“…HvINT-C) on grain weight, grain number and grain yield (Liller et al, 2015). Another common interaction occurs between flowering time and yield components, as reported by (Maurer et al, 2016;Mikolajczak et al, 2016;Wang et al, 2016). One alternative to model these interactions is to express explicitly the sensitivity of genes to environmental conditions via ecophysiological models, as shown for flowering time in barley by , or via graphical models and structural relations models (Wang & van Eeuwijk, 2014;Wang et al, 2015;Alimi, 2016).…”

Construction of a high-density genetic map and fine mapping of a candidate gene locus for a novel branched-spike mutant in barley

“…Many high-density genetic maps have been constructed using SSR, DarT and SNP markers for different barley populations [21][22][29][30][31]. Of them, the high-density genetic map constructed by Wang et al [21] had relatively high quality, with 1,375.8 cM length and a 0.7 cM mean adjacent marker distance. Compared with other genetic maps, the map reported in the present paper had significantly improved marker density and marker uniformity.…”

“…Therefore, SNP identification and genotyping based on simplified sequencing is a reasonable choice for high-density map construction and gene or QTL finemapping in barley. Chutimanitsakun et al successfully fine-mapped the QTLs of plant height, spike length and grain number per spike using SNPs developed from RAD-seq(restriction-site associated DNA sequence) [20][21][22]. Zhou et al [23] developed 12,998 SLAF markers and constructed a high-density genetic map with a total genetic distance of 967.6 cM.…”