Abstract
Main conclusion
Meta-analysis in wheat for three major quality traits identified 110 meta-QTL (MQTL) with reduced confidence interval (CI). Five GWAS validated MQTL (viz., 1A.1, 1B.2, 3B.4, 5B.2, and 6B.2), each involving more than 20 initial QTL and reduced CI (95%) (< 2 cM), were selected for quality breeding programmes. Functional characterization including candidate gene mining and expression analysis discovered 44 high confidence candidate genes associated with quality traits.
Abstract
A meta-analysis of quantitative trait loci (QTL) associated with dough rheology properties, nutritional traits, and processing quality traits was conducted in wheat. For this purpose, as many as 2458 QTL were collected from 50 interval mapping studies published during 2013–2020. Of the total QTL, 1126 QTL were projected onto the consensus map saturated with 249,603 markers which led to the identification of 110 meta-QTL (MQTL). These MQTL exhibited an 18.84-fold reduction in the average CI compared to the average CI of the initial QTL (ranging from 14.87 to 95.55 cM with an average of 40.35 cM). Of the 110, 108 MQTL were physically anchored to the wheat reference genome, including 51 MQTL verified with marker-trait associations (MTAs) reported from earlier genome-wide association studies. Candidate gene (CG) mining allowed the identification of 2533 unique gene models from the MQTL regions. In-silico expression analysis discovered 439 differentially expressed gene models with > 2 transcripts per million expressions in grains and related tissues, which also included 44 high-confidence CGs involved in the various cellular and biochemical processes related to quality traits. Nine functionally characterized wheat genes associated with grain protein content, high-molecular-weight glutenin, and starch synthase enzymes were also found to be co-localized with some of the MQTL. Synteny analysis between wheat and rice MQTL regions identified 23 wheat MQTL syntenic to 16 rice MQTL associated with quality traits. Furthermore, 64 wheat orthologues of 30 known rice genes were detected in 44 MQTL regions. Markers flanking the MQTL identified in the present study can be used for marker-assisted breeding and as fixed effects in the genomic selection models for improving the prediction accuracy during quality breeding. Wheat orthologues of rice genes and other CGs available from MQTLs can be promising targets for further functional validation and to better understand the molecular mechanism underlying the quality traits in wheat.
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Abbreviations
- CG:
-
Candidate gene
- CI:
-
Confidence interval
- DEGs:
-
Differentially expressed genes
- GPC:
-
Grain protein content
- GWAS:
-
Genome-wide association studies
- MQTL:
-
Meta-QTL
- MTA:
-
Marker-trait association
- PPO:
-
Poly phenol oxidase
- TPM:
-
Transcripts per million
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Acknowledgements
Thanks are due to the Minority Welfare Department, Government of Karnataka, India for providing Ph.D. fellowship to SG and to Department of Science and Technology (DST), New Delhi, India for providing INSPIRE fellowship to DKS and to Head, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, (India) for providing necessary facilities.
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Fig. S1
Salient features of the initial QTL. a Number of QTL available from different chromosomes. b Size of the populations utilized for mapping. c Number of different types of populations. d Different types of markers utilized for mapping. e Methods employed for mapping in different studies. f Phenotypic variation explained (PVE). g LOD scores. h Peak positions of the QTL. Supplementary file1 (TIF 1626 KB)
Fig. S2
Characteristic features of the meta-QTL (MQTL). a Distribution of MQTL identified on different wheat chromosomes. b Trait-wise distribution of the MQTL. c Average CIs of initial QTL and MQTL and fold reduction in CI values after MQTL analysis. d Different number of QTL involved in MQTL. (e) MQTL associated with the different number of traits. Supplementary file2 (TIF 1975 KB)
Fig. S3
Expression pattern of 44 high-confidence candidate genes (CGs) in the different relevant tissues. Supplementary file3 (TIFF 1270 KB)
Fig. S4
Circular diagram representing the conserved regions between wheat and rice MQTL. Supplementary file4 (TIFF 2892 KB)
Fig. S5
The syntenic region of MQTL between the wheat and rice. The genomic position, chromosome number, and shared genes between wheat and rice are indicated. Supplementary file5 (TIF 576 KB)
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Gudi, S., Saini, D.K., Singh, G. et al. Unravelling consensus genomic regions associated with quality traits in wheat using meta-analysis of quantitative trait loci. Planta 255, 115 (2022). https://doi.org/10.1007/s00425-022-03904-4
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DOI: https://doi.org/10.1007/s00425-022-03904-4