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Detection of candidate genes and development of KASP markers for Verticillium wilt resistance by combining genome-wide association study, QTL-seq and transcriptome sequencing in cotton

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Combining GWAS, QTL-seq and transcriptome sequencing detected basal defense-related genes showing gDNA sequence variation and expression difference in diverse cotton lines, which might be the molecular mechanisms of VW resistance in G. hirsutum.

Abstract

Verticillium wilt (VW), which is caused by the soil-borne fungus Verticillium dahliae, is a major disease in cotton (Gossypim hirsutum) worldwide. To facilitate the understanding of the genetic basis for VW resistance in cotton, a genome-wide association study (GWAS), QTL-seq and transcriptome sequencing were performed. The GWAS of VW resistance in a panel of 120 core elite cotton accessions using the Cotton 63K Illumina Infinium SNP array identified 5 QTL from 18 significant SNPs meeting the 5% false discovery rate threshold on 5 chromosomes. All QTL identified through GWAS were found to be overlapped with previously reported QTL. By combining GWAS, QTL-seq and transcriptome sequencing, we identified eight candidate genes showing both gDNA sequence variation and expression difference between resistant and susceptible lines, most related to transcription factors (TFs), flavonoid biosynthesis and those involving in the plant basal defense and broad-spectrum disease resistance. Ten KASP markers were successfully validated in diverse cotton lines and could be deployed in marker-assisted breeding to enhance VW resistance. These results supported our inference that the gDNA sequence variation or expression difference of those genes involving in the basal defense in diverse cotton lines might be the molecular mechanisms of VW resistance in G. hirsutum.

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Ackonwledgements

The authors thank professor Heqin Zhu for supplying the pathogenic strain of V. dahliae and the technical support in identifying disease resistance, and thank Dr Yuhui Xu for giving professional advices in analysing the data using different models.This study was supported by the National Key R&D Program of China (2018YFD0100301 and 2017YFD0101600) and the Central Public-interest Scientific Institution Basal Research Fund (No. 1610162020040905).

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HW, PZ, and YZ conceived and designed the experiments; YZ, WC, YC, XS, and JL executed the experiments; YZ analysed the data and wrote the paper; HJ and WW contributed reagents, materials, and analysis tools.

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Correspondence to Pei Zhao or Hongmei Wang.

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Communicated by Brent Hulke.

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Zhao, Y., Chen, W., Cui, Y. et al. Detection of candidate genes and development of KASP markers for Verticillium wilt resistance by combining genome-wide association study, QTL-seq and transcriptome sequencing in cotton. Theor Appl Genet 134, 1063–1081 (2021). https://doi.org/10.1007/s00122-020-03752-4

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