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Meta-QTLs, ortho-meta-QTLs and candidate genes for grain yield and associated traits in wheat (Triticum aestivum L.)

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Abstract

Key message

In wheat, 2852 major QTLs of 8998 QTLs available for yield and related traits were used for meta-analysis; 141 meta-QTLs were identified, which included 13 breeder’s MQTLs and 24 ortho-MQTLs; 1202 candidate genes and 50 homologues of genes for yield from other cereals were also identified.

Abstract

Meta-QTL analysis was conducted using 2852 of the 8998 known QTLs, retrieved from 230 reports published during 1999–2020 (including 19 studies on tetraploid wheat) for grain yield (GY) and the following ten component traits: (i) grain weight (GWei), (ii) grain morphology-related traits (GMRTs), (iii) grain number (GN), (iv) spikes-related traits (SRTs), (v) plant height (PH), (vi) tiller number (TN), (vii) harvest index (HI), (viii) biomass yield (BY), (ix) days to heading/flowering and maturity (DTH/F/M), and (x) grain filling duration (GFD). The study resulted in the identification of 141 meta-QTLs (MQTLs), with an average confidence interval (CI) of 1.4 cM as against a CI of > 12.1 cM (8.8 fold reduction) in the QTLs that were used. The corresponding physical length of CI ranged from 0.01 Mb to 661.9 Mb (mean, 31.5 Mb). Seventy-seven (77) of these 141 MQTLs overlapped marker-trait associations (MTAs) reported in genome-wide association studies. Also, 63 MQTLs (each based on at least 10 QTLs) were considered stable and robust, with 13 MQTLs described as breeder’s MQTLs (selected based on small CI, large LOD, and high level of phenotypic variation explained). Thirty-five yield-related genes from rice, barley, and maize were also utilized to identify 50 wheat homologues in MQTLs. Further, the use of synteny and collinearity allowed the identification of 24 ortho-MQTLs which were common among the wheat, barley, rice, and maize. The results of the present study should prove useful for wheat breeding and future basic research in cereals including wheat, barley, rice, and maize.

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Availability of data and material

Data generated or analysed during this study are included in this published article (and its Supplementary material 1). Datasets are also available from the corresponding author on reasonable request.

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Acknowledgements

Thanks are due to the 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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This research received no external funding.

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Authors and Affiliations

  1. Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India

    Dinesh Kumar Saini & Puja Srivastava

  2. Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India

    Neeraj Pal

  3. Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India

    P. K. Gupta

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  1. Dinesh Kumar Saini
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  2. Puja Srivastava
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  3. Neeraj Pal
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  4. P. K. Gupta
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Contributions

P.S., P.K.G. and D.K.S. conceived and designed the project; P.K.G. and P.S. supervised the study; D.K.S. and N.P. conducted the analysis; D.K.S. wrote the paper and P.K.G. and P.S. corrected the final draft. All authors read and approved the final manuscript.

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Correspondence to Puja Srivastava.

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Communicated by Xianchun Xia.

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Saini, D.K., Srivastava, P., Pal, N. et al. Meta-QTLs, ortho-meta-QTLs and candidate genes for grain yield and associated traits in wheat (Triticum aestivum L.). Theor Appl Genet 135, 1049–1081 (2022). https://doi.org/10.1007/s00122-021-04018-3

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