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Genome-wide analysis of CrRLK1L gene family in Gossypium and identification of candidate CrRLK1L genes related to fiber development

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Abstract

Members of the CrRLK1L family, a subgroup of the receptor-like kinase (RLK) gene family, are thought to act as sensors for the integrity of the cell wall and regulators of polar elongation. To better understand the various functions in fiber development, we conducted genome-wide identification and characterization analyses of CrRLK1L family in cotton. Here 44, 40, and 79 CrRLK1L genes were identified from three cotton species: diploid G. raimondii (D5), diploid G. arboreum (A2), and tetraploid G. hirsutum TM-1 (AD1), respectively. The 44 CrRLK1Ls in G. raimondii were anchored to the 12 chromosomes unevenly and were classified into six groups (I–VI), with group II and group IV being further divided into two subgroups (groups IIa and IIb, and IVa and IVb, respectively). These CrRLK1Ls displayed a highly regular pattern of developmental and spatial regulation in cotton. Using the transcriptome data of five chromosomal segment introgression lines (CSILs) and the physical integration of CrRLK1Ls with the quantitative trait loci (QTLs) related to fiber quality traits, we revealed that six CrRLK1L genes were highly associated with fiber development. This study brings new insights into the integrated genome-wide identification of CrRLK1Ls in cotton and provides references for the genetic improvement of cotton fiber.

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Abbreviations

RLKs:

Receptor-like kinases

DPA:

Days post anthesis

qRT-PCR:

Quantitative real-time PCR

TAIR:

The Arabidopsis information resource

BLAST:

Basic local alignment search tool

CSILs:

Chromosomal segment introgression lines

QTLs:

Quantitative trait loci

FPKM:

Fragments per kilobase of exon model per million mapped reads

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Acknowledgments

This program was financially supported in part by the National Natural Science Foundation of China (31471539), the National High Technology Research and Development Program of China (863 Program) (2012AA101108-04-04), the Key R & D program in Jiangsu Province (BE2015360), the Six talent peaks project in Jiangsu province (2015-NY-002), the Priority Academic Program Development of Jiangsu Higher Education Institutions (010-809001) and the JCIC-MCP project (No. 10).

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  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China

    Erli Niu, Caiping Cai, Yongjie Zheng, Xiaoguang Shang, Lei Fang & Wangzhen Guo

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  1. Erli Niu
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  2. Caiping Cai
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Correspondence to Wangzhen Guo.

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Fig. S1 Multiple sequence alignments of amino acids for 44 GrCrRLK1L genes (TIFF 5797 kb)

438_2016_1169_MOESM2_ESM.tiff

Fig. S2 Correlation analysis of the expression patterns obtained through expression profiling and qRT-PCR. Three cotton genes, GhEF1α (a), GhHis3 (b), and GhTub1 (c), were used as reference controls for qRT-PCR analysis. The X axis indicates the FPKM of expression profiling and the Y axis indicates the relative expression level of qRT-PCR (TIFF 156 kb)

Table S1 Gene primers used in this study (XLSX 14 kb)

Table S2 Sequence similarity and expression correlation of CrRLK1L genes in cotton (XLSX 20 kb)

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Niu, E., Cai, C., Zheng, Y. et al. Genome-wide analysis of CrRLK1L gene family in Gossypium and identification of candidate CrRLK1L genes related to fiber development. Mol Genet Genomics 291, 1137–1154 (2016). https://doi.org/10.1007/s00438-016-1169-0

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