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QTL analysis and candidate gene identification for plant height in cotton based on an interspecific backcross inbred line population of Gossypium hirsutum × Gossypium barbadense

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Abstract

Key message

We constructed the first high-quality and high-density genetic linkage map for an interspecific BIL population in cotton by specific-locus amplified fragment sequencing for QTL mapping. A novel gene GhPIN3 for plant height was identified in cotton.

Abstract

Ideal plant height (PH) is important for improving lint yield and mechanized harvesting in cotton. Most published genetic studies on cotton have focused on fibre yield and quality traits rather than PH. To facilitate the understanding of the genetic basis in PH, an interspecific backcross inbred line (BIL) population of 250 lines derived from upland cotton (Gossypium hirsutum L.) CRI36 and Egyptian cotton (G. barbadense L.) Hai7124 was used to construct a high-density genetic linkage map for quantitative trait locus (QTL) mapping. The high-density genetic map harboured 7,709 genotyping-by-sequencing (GBS)-based single nucleotide polymorphism (SNP) markers that covered 3,433.24 cM with a mean marker interval of 0.67 cM. In total, ten PH QTLs were identified and each explained 4.27–14.92% of the phenotypic variation, four of which were stable as they were mapped in at least two tests or based on best linear unbiased prediction in seven field tests. Based on functional annotation of orthologues in Arabidopsis and transcriptome data for the genes within the stable QTL regions, GhPIN3 encoding for the hormone auxin efflux carrier protein was identified as a candidate gene located in the stable QTL qPH-Dt1-1 region. A qRT-PCR analysis showed that the expression level of GhPIN3 in apical tissues was significantly higher in four short-statured cotton genotypes than that in four tall-statured cotton genotypes. Virus-induced gene silencing cotton has significantly increased PH when the expression of the GhPIN3 gene was suppressed.

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Acknowledgements

The authors wish to thank New Mexico Agricultural Experiment Station, New Mexico, USA. This research was supported by grants from the National Natural Science Foundation of China (Grant Nos. 31621005 and 31701474), the National Key Research and Development Program of China (Grant Nos. 2018YFD0100300 and 2016YFD0101400).

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  1. Jianjiang Ma and Wenfeng Pei have contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China

    Jianjiang Ma, Qifeng Ma, Yanhui Geng, Guoyuan Liu, Ji Liu, Yupeng Cui, Xia Zhang, Man Wu, Xingli Li, Dan Li, XinShan Zang, Jikun Song, Shurong Tang, Shuxun Yu & Jiwen Yu

  2. Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 880033, USA

    Jinfa Zhang

  3. College of Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China

    Jianjiang Ma & Shuxun Yu

  4. Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830001, China

    Wenfeng Pei

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Supplemental Figure S1

SLAF markers number and fold depth for each of the BILs and their parents. In a and b, the red, green and blue represent recurrent parent CRI36, parent Hai7124 and offspring, respectively. (PDF 441 kb)

Supplemental Figure S2

Marker collinearity between the genetic map and the physical one. a and b represent the marker collinearity in the A subgenome and D subgenome, respectively. (TIFF 4487 kb)

Supplemental Figure S3

Information on QTL mapping. a shows the QTL in At3 detected with BLUP; b shows the QTL in At10 detected in 16Hnsy; c shows the QTL in Dt9 detected in 17Aync; d shows the QTL in Dt11 detected in 16Aync; d shows the QTL in Dt12 detected in 16Aync; e shows the QTL in Dt13 detected in 17Aync; the black dotted line represents LOD = 3.50; the red line represents the percentage of phenotypic variance explained; and the blue line represents the LOD value. (PDF 560 kb)

Supplemental Table S1

ANOVA and combined broad-sense heritability analysis of plant height. (XLSX 10 kb)

Supplemental Table S2

Genotype statistics of SNP markers in the two parents. (XLSX 8 kb)

Supplemental Table S3

Genotype frequency information of the 7,709 SNP markers in the genetic map. 6 (XLSX 8 kb)

Supplemental Table S4

The 7,709 markers and their genetic distance information in the genetic map. 7 (XLSX 200 kb)

Supplemental Table S5

The physical position information of the 7,709 markers. 8 (XLSX 211 kb)

Supplemental Table S6

Spearman correlation coefficient between the genetic map and physical map in each linkage group. 9 (XLSX 9 kb)

Supplemental Table S7

The position information of the 336 recombination hotspots in the genetic map 10 (XLSX 30 kb)

Supplemental Table S8

Gene annotation analysis of 1,220 candidate genes 11 (XLSX 60 kb)

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Ma, J., Pei, W., Ma, Q. et al. QTL analysis and candidate gene identification for plant height in cotton based on an interspecific backcross inbred line population of Gossypium hirsutum × Gossypium barbadense. Theor Appl Genet 132, 2663–2676 (2019). https://doi.org/10.1007/s00122-019-03380-7

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