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. 2019 Jul 22;20(1):599.
doi: 10.1186/s12864-019-5819-6.

A high density SLAF-seq SNP genetic map and QTL for seed size, oil and protein content in upland cotton

Wenwen Wang  1 , Ying Sun  1 , Peng Yang  1 , Xiaoyan Cai  2 , Le Yang  1 , Junrui Ma  1 , Yuncan Ou  1 , Tianpeng Liu  1 , Iftikhar Ali  1 , Dajun Liu  1 , Jian Zhang  1 , Zhonghua Teng  1 , Kai Guo  1 , Dexin Liu  1 , Fang Liu  3 , Zhengsheng Zhang  4
Affiliations

A high density SLAF-seq SNP genetic map and QTL for seed size, oil and protein content in upland cotton

Wenwen Wang et al. BMC Genomics. .

Abstract

Background: Cotton is a leading natural fiber crop. Beyond its fiber, cottonseed is a valuable source of plant protein and oil. Due to the much higher value of cotton fiber, there is less consideration of cottonseed quality despite its potential value. Though some QTL controlling cottonseed quality have been identified, few of them that warrant further study are known. Identifying stable QTL controlling seed size, oil and protein content is necessary for improvement of cottonseed quality.

Results: In this study, a recombinant inbred line (RIL) population was developed from a cross between upland cotton cultivars/lines Yumian 1 and M11. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to construct a genetic map that covered 3353.15 cM with an average distance between consecutive markers of 0.48 cM. The seed index, together with kernel size, oil and protein content were further used to identify QTL. In total, 58 QTL associated with six traits were detected, including 13 stable QTL detected in all three environments and 11 in two environments.

Conclusion: A high resolution genetic map including 7033 SNP loci was constructed through specific locus amplified fragment sequencing technology. A total of 13 stable QTL associated with six cottonseed quality traits were detected. These stable QTL have the potential for fine mapping, identifying candidate genes, elaborating molecular mechanisms of cottonseed development, and application in cotton breeding programs.

Keywords: Oil; Protein; QTL; SLAF-seq; Seed size; Upland cotton.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Genetic maps and QTL for cottonseed quality in the Yumian 1 × M11 RIL population
See this image and copyright information in PMC

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