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Genomic map** and identification of candidate genes encoding nulliplex-branch trait in sea-island cotton (Gossypium barbadense L.) by multi-omics analysis

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Abstract

Nulliplex branch is a key architectural trait in sea-island cotton (Gossypium barbadense L.), but its genetic basis is not well understood. Here we investigated the genetic basis of the nulliplex-branch trait in cotton by combining newly created bulked segregant analysis (BSA)-seq data, published RNA-seq data, and published whole-genome resequencing (WGR) data. We delimited the nulliplex-branch locus (qD07-NB) to D07, region 14.8–17.1 Mb, using various BSA methods and markers. We integrated our BSA data with WGR data of sea-island cotton varieties and detected a missense single-nucleotide polymorphism in the candidate gene (Gbar_D07G011870) of qD07-NB. This gene was under positive selection during sea-island cotton breeding in the **njiang Uygur Autonomous Region, China. Notably, the nulliplex-branch varieties possessed a better fiber quality than the long-branch varieties, and a set of high-quality molecular markers was identified for molecular breeding of the nulliplex-branch trait in cotton. We combined BSA-seq and RNA-seq data to compare gene expression profiles between two elite sea-island cotton varieties during three developmental stages. We identified eleven relevant candidate genes, five downregulated and six upregulated, in the qD07-NB locus. This research will expand our understanding of the genetic basis of the nulliplex-branch trait and provide guidance for architecture-focused breeding in cotton.

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Acknowledgements

We would like to acknowledge Prof. Zhongxu Lin in Huazhong Agricultural University for providing a platform to analyze the BSA-seq data.

Funding

This work was supported by the National Natural Science Foundation of China (Grant no. 31460362) and Science and Technology Research Project of the Education Department of Jiangxi Province, China (Grant no. GJJ200440).

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Authors and Affiliations

  1. Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China

    Tianwang Wen, Mengxing Wang & Feiyu Tang

  2. College of Plant Science, Tarim University, Alaer, 843300, **njiang, China

    Chunyan Liu, Tianyou Wang & Liangrong He

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  1. Tianwang Wen
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Contributions

Liangrong He designed this program and performed the experiment. Feiyu Tang and Mengxing Wang revised the manuscript. Tianwang Wen analyzed the data and drafted the manuscript. Chunyan Liu and Tianyou Wang conducted the field investigation. All the authors read and approved the final version of the manuscript.

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Tianwang Wen and Chunyan Liu are co-first authors.

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Wen, T., Liu, C., Wang, T. et al. Genomic map** and identification of candidate genes encoding nulliplex-branch trait in sea-island cotton (Gossypium barbadense L.) by multi-omics analysis. Mol Breeding 41, 34 (2021). https://doi.org/10.1007/s11032-021-01229-w

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