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QTL delineation for five fiber quality traits based on an intra-specific Gossypium hirsutum L. recombinant inbred line population

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Abstract

Gossypium hirsutum L. is the most important fiber crop worldwide and contributes to more than 95% of global cotton production. Marker-assisted selection (MAS) is an effective approach for improving fiber quality, and quantitative trait loci (QTL) mapping of fiber quality traits is important for cotton breeding. In this study, a permanent intra-specific recombinant inbred line (RIL) population containing 137 families was used for fiber quality testing. Based on a previously reported high-density genetic map with an average marker distance of 0.63 cM, 186 additive QTLs were obtained for five fiber quality traits over five consecutive years, including 39 for fiber length (FL), 36 for fiber strength (FS), 50 for fiber uniformity (FU), 33 for micronaire (MC) and 28 for fiber elongation (FE). Three stable QTLs, qMC-A4-1, qMC-D2-3 and qFS-D9-1, were detected in four datasets, and another eight stable QTLs, qMC-A4-2, qMC-D11-2, qFU-A9-1, qFU-A10-4, qFS-D11-1, qFL-D9-2, qFL-D11-1 and qFE-A3-2, were detected in three datasets. The annotated genes in these 11 stable QTLs were collected, and these genes included many transcription factors with functions during fiber development. 33 QTL coincidence regions were found, and these involved nearly half of the total QTLs. Four chromosome regions containing at least 6 QTLs were promising for fine mapping. In addition, 41 pairs of epistatic QTLs (e-QTLs) were screened, including 6 for FL, 30 for FS, 2 for FU and 3 for MC. The identification of stable QTLs adds valuable information for further QTL fine mapping and gene positional cloning for fiber quality genetic detection and provides useful markers for further molecular breeding in enhancing fiber quality.

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Abbreviations

RAD-seq:

Restriction-site associated DNA sequencing

SNP:

Single nucleotide polymorphism

QTL:

Quantitative trait locus

QCR:

QTL coincidence region

PV:

Phenotypic variation

RIL:

Recombinant inbred line

FE:

Fiber elongation

FL:

Fiber length

FS:

Fiber strength

FU:

Fiber uniformity

MC:

Micronaire

MAS:

Marker-assisted selection

e-PCR:

Electronic PCR

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Acknowledgements

This work was funded by the Major Program of the National Natural Science Foundation of China (No. 31690093) and the Science and Technology Development by Henan province (No. 162102110020). The experiment was performed at the State Key Laboratory of Cotton Biology in the Institute of Cotton Research of the Chinese Academy of Agricultural Sciences.

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  1. Xiaoyun Jia and Hantao Wang authors have contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China

    Xiaoyun Jia, Hantao Wang, Chaoyou Pang, Qifeng Ma, Junji Su, Hengling Wei, Meizhen Song, Shuli Fan & Shuxun Yu

  2. Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China

    Xiaoyun Jia

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  1. Xiaoyun Jia
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  2. Hantao Wang
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Contributions

Shuxun Yu, Shuli Fan, Meizhen Song and Chaoyou Pang designed the experiment. Xiaoyun Jia and Hantao Wang performed the experiment. Hengling Wei and Xiaoyun Jia analyzed the phenotypic data. Xiaoyun Jia and Hantao Wang performed the QTL analysis. Xiaoyun Jia wrote and revised the manuscript. All the authors read and approved the final manuscript.

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Correspondence to Shuxun Yu.

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This article does not describe any studies with human participants or animals performed by any of the authors.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

438_2018_1424_MOESM1_ESM.xls

Supplemental file 1 Total QTLs of the five fiber quality traits. FL, fiber length; FS, fiber strength; FU, fiber uniformity; MC, micronaire; FE, fiber elongation (XLS 68 KB)

Supplemental file 2 Annotations in 11 valuable QTL regions (XLS 905 KB)

438_2018_1424_MOESM3_ESM.pdf

Supplemental file 3 All QTL coincidence regions on the genetic map. FL, fiber length; FS, fiber strength; FU, fiber uniformity; MC, micronaire; FE, fiber elongation (PDF 308 KB)

438_2018_1424_MOESM4_ESM.xls

Supplemental file 4 Epistatic QTLs of four fiber quality traits. FL, fiber length; FS, fiber strength; FU, fiber uniformity; MC, micronaire (XLS 51 KB)

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Jia, X., Wang, H., Pang, C. et al. QTL delineation for five fiber quality traits based on an intra-specific Gossypium hirsutum L. recombinant inbred line population. Mol Genet Genomics 293, 831–843 (2018). https://doi.org/10.1007/s00438-018-1424-7

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