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Genomic associations for drought tolerance on the short arm of wheat chromosome 4B

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Abstract

Drought is a major constraint to maintaining yield stability of wheat in rain fed and limited irrigation agro-ecosystems. Genetic improvement for drought tolerance in wheat has been difficult due to quantitative nature of the trait involving multiple genes with variable effects and lack of effective selection strategies employing molecular markers. Here, a framework molecular linkage map was constructed using 173 DNA markers randomly distributed over the 21 wheat chromosomes. Grain yield and other drought-responsive shoot and root traits were phenotyped for 2 years under drought stress and well-watered conditions on a mapping population of recombinant inbred lines (RILs) derived from a cross between drought-sensitive semidwarf variety “WL711” and drought-tolerant traditional variety “C306”. Thirty-seven genomics region were identified for 10 drought-related traits at 18 different chromosomal locations but most of these showed small inconsistent effects. A consistent genomic region associated with drought susceptibility index (qDSI.4B.1) was mapped on the short arm of chromosome 4B, which also controlled grain yield per plant, harvest index, and root biomass under drought. Transcriptome profiling of the parents and two RIL bulks with extreme phenotypes revealed five genes underlying this genomic region that were differentially expressed between the parents as well as the two RIL bulks, suggesting that they are likely candidates for drought tolerance. Syntenic genomic regions of barley, rice, sorghum, and maize genomes were identified that also harbor genes for drought tolerance. Markers tightly linked to this genomic region in combination with other important regions on group 7 chromosomes may be used in marker-assisted breeding for drought tolerance in wheat.

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Acknowledgments

We are thankful to the Indian Council of Agricultural Research for financial support under the NPTC project.

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Correspondence to Nagendra Singh.

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Table S1

Variation in trait values for the parental lines and RILs for grain yield per plant (GY), drought susceptibility index (DSI) for yield, harvest index (HI), shoot biomass (SB), plant height (PH), days to flowering (DTF), maximum root length (MRL), total root biomass (TRB), root biomass up to 30 cm (RBU30), and root biomass below 30 cm (RBB30) in 2 years under drought and control conditions (DOC 69 kb)

Table S2

QTLs for different drought-related traits identified by QTL Network software in 206 RILs derived from cross between wheat varieties WL711 and C306 grown in pipes under drought conditions (DOC 88 kb)

Table S3

QTLs for different drought-related traits identified by QTL Network software in 206 RILs derived from cross between wheat varieties WL711 and C306, grown in pipes under control conditions (DOC 74 kb)

Table S4

Epistatic QTLs and QTL × QTL × environment interactions for different drought-related traits identified by two locus analysis using QTL Network software in 206 RILs derived from cross between wheat varieties WL711 and C306 grown in pipes under drought conditions (DOC 57 kb)

Table S5

Epistatic QTLs and QTL × QTL × environment interactions for different drought-related traits identified by two locus analysis using QTL Network software in 206 RILs derived from cross between wheat varieties WL711 and C306 grown in pipes under control conditions (DOC 56 kb)

Table S6

Meta-QTL for drought-related traits under drought and control conditions identified by meta-analysis (DOC 60 kb)

Table S7

Annotation of genes commonly differentially expressed between drought-tolerant and sensitive RIL bulks as well as between tolerant and sensitive parents. Genes located in the wheat chromosome bins spanning the QTL interval qDSI.4B.1 are underlined and those with more than fivefold change in expression are shaded. (DOC 180 kb)

Table S8

Homologues of common differentially expressed genes between two parents and RIL bulks in the syntenic regions of rice, sorghum, and maize chromosomes. Genes in bold are bin mapped in the qDSI.4B.1 region of wheat (DOC 83 kb)

Fig. S1

Meta-QTLs identified on chromosomes 4B by meta-analysis of reported drought-responsive traits QTLs in this study. The picture shows the meta-QTLs on chromosomes 4B. Vertical lines on the left of chromosomes indicate the confidence interval, horizontal lines indicate the variance, MQTL are in red. Markers and genetic distance (cM) are shown on the right of chromosomes (DOC 460 kb)

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Kadam, S., Singh, K., Shukla, S. et al. Genomic associations for drought tolerance on the short arm of wheat chromosome 4B. Funct Integr Genomics 12, 447–464 (2012). https://doi.org/10.1007/s10142-012-0276-1

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