Meta-QTL analysis and identification of candidate genes for multiple-traits associated with spot blotch resistance in bread wheat

Abstract

In bread wheat, a literature search gave 228 QTLs for six traits, including resistance against spot blotch and the following five other related traits: (i) stay green; (ii) flag leaf senescence; (iii) green leaf area duration; (iv) green leaf area of the main stem; and (v) black point resistance. These QTLs were used for metaQTL (MQTL) analysis. For this purpose, a consensus map with 72,788 markers was prepared; 69 of the above 228 QTLs, which were suitable for MQTL analysis, were projected on the consensus map. This exercise resulted in the identification of 16 meta-QTLs (MQTLs) located on 11 chromosomes, with the PVE ranging from 5.4% (MQTL7) to 21.8% (MQTL5), and the confidence intervals ranging from 1.5 to 20.7 cM (except five MQTLs with a range of 36.1-57.8 cM). The number of QTLs associated with individual MQTLs ranged from a maximum of 17 in MQTL3 to 8 each in MQTL5 and MQTL8 and 5 each in MQTL7 and MQTL14. The 16 MQTLs, included 12 multi-trait MQTLs; one of the MQTL also overlapped a genomic region carrying the major spot blotch resistance gene Sb1. Of the total 16 MQTLs, 12 MQTLs were also validated through marker-trait associations that were available from earlier genome-wide association studies. The genomic regions associated with MQTLs were also used for the identification of candidate genes (CGs) and led to the identification of 516 CGs encoding 508 proteins; 411 of these proteins are known to be associated with resistance against several biotic stresses. In silico expression analysis of CGs using transcriptome data allowed the identification of 71 differentially expressed CGs, which were examined for further possible studies. The findings of the present study should facilitate fine-mapping and cloning of genes, enabling Marker Assisted Selection.

Keywords: Bipolaris sorokiniana; Candidate genes; Meta-QTL; Spot blotch; Wheat.

Figure 1

The data utilised in the MQTL analysis. (a) frequencies of QTLs used to identify MQTLs on each of the 20 wheat chromosomes (except 6B); (b) frequencies of QTLs with different LOD scores; (c) frequencies of QTLs for different traits; (d) density of molecular markers on consensus map involving 21 wheat chromosomes; (e) frequencies of QTLs with different PVE% values.

Figure 2

MQTLs are distributed on various wheat chromosomes, with MQTLs shown by blue and GWAS validated MQTLs indicated by red.

Figure 3

(a) Gene ontology (GO) for differentially expressed candidate genes (DECGs) identified in the present study; (b) Heat maps exhibiting 71 DECGs that encoded important proteins and are associated with the MQTLs. The scale shown on the top of left of the heat map shows the fold change value that varies in the heat-maps proteins encoded by DECGs.