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A comparative transcriptome analysis of two sets of backcross inbred lines differing in lint-yield derived from a Gossypium hirsutum × Gossypium barbadense population

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Abstract

Upland cotton (Gossypium hirsutum L.) is the most important fiber crop, and its lint-yield improvement is impeded due to its narrow genetic base and the lack of understanding of the genetic basis of yield. Backcross inbred lines (BILs) or near-isogenic lines (NILs) in the same genetic background differing in lint yield, developed through advanced backcrossing, provide an important genomic resource to study the molecular genetic basis of lint yield. In the present study, a high-yield (HY) group and a low-yield (LY) group each with three BILs were selected from a BIL population between G. hirsutum and G. barbadense. Using a microarray-based comparative transcriptome analysis on developing fibers at 10 days post-anthesis (DPA) between the two groups, 1486 differentially expressed genes (DEGs) were identified. A total of 212 DEGs were further mapped in the regions of 24 yield QTL and 11 yield trait QTL hotspots as reported previously, and 81 DEGs mapped with the 7 lint-yield QTL identified in the BIL population from which the two sets of BILs were selected. Gene Ontology annotations and Blast-Mapping-Annotation-KEGG analysis via Blast2GO revealed that more DEGs were associated with catalytic activity and binding, followed by transporters, nucleic acid binding transcription factors, structural molecules and molecular transducer activities. Six DEGs were chosen for a quantitative RT-PCR assay, and the results were consistent with the microarray analysis. The development of DEGs-based markers revealed that 7 single strand conformation polymorphism-based single nucleotide polymorphic (SSCP-SNP) markers were associated with yield traits, and 3 markers with lint yield. In the present study, we identified a number of yield and yield component QTL-co-localizing DEGs and developed several DEG-based SSCP-SNP markers for the traits, thereby providing a set of candidate genes for molecular breeding and genetic manipulation of lint yield in cotton.

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Abbreviations

HY:

High-yield

LY:

Low-yield

HYP:

HY parent

LYP:

LY parent

DEGs:

Differentially expressed genes

NILs:

Near isogenic lines

DPA:

Days post-anthesis

QTL:

Quantitative trait loci

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Acknowledgments

The research was sponsored by a grant from the National Natural Science Foundation of China (Grant 31301367 and Grant 31301368) and the 863 National High-Tech Research Development Program in China (Grant 2012AA101108). The research was also in part supported by the New Mexico Agricultural Experiment Station.

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Authors and Affiliations

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

    Wu Man, Liyuan Zhang, Xihua Li, Xiaobing Xie, Wenfeng Pei, Jiwen Yu & Shuxun Yu

  2. Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA

    Jinfa Zhang

  3. Wuyang A & F Bureau, Luohe, Henan, China

    Xiaobing Xie

Authors
  1. Wu Man
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  2. Liyuan Zhang
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  3. Xihua Li
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  4. Xiaobing Xie
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  5. Wenfeng Pei
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  6. Jiwen Yu
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  7. Shuxun Yu
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  8. Jinfa Zhang
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Corresponding authors

Correspondence to Jiwen Yu, Shuxun Yu or Jinfa Zhang.

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Funding

This study was funded by the National Natural Science Foundation of China (Grant Nos. 31301367; 31301368) and the 863 National High-Tech Research Development Program in China (Grant No. 2012AA101108).

Conflict of interest

The authors declare that they no conflict of interest.

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This article does not contain 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.

Supplementary Data 1. Primers used for RT-PCR and qRT-PCR analyses (XLSX 11 kb)

438_2016_1216_MOESM2_ESM.xlsx

Supplementary Data 2. Primer sequences for 45 genes used for the analysis of single strand conformation polymorphism (SSCP)-based single nucleotide polymorphic (SNP) markers (XLSX 14 kb)

438_2016_1216_MOESM3_ESM.xlsx

Supplementary Data 3. Microarray results for the differentially expressed genes (DEGs) identified in the high- and low-yield groups (XLSX 178 kb)

438_2016_1216_MOESM4_ESM.xlsx

Supplementary Data 4. Mapping of DEGs with the 24 yield QTL and 12 yield trait QTL hotspots on the genomes of G. hirsutum (XLSX 68 kb)

Supplementary Data 5. 212 mapped DEGs in the 24 yield QTL and 12 yield trait QTL hotspots (XLSX 45 kb)

Supplementary Data 6. 81 mapped DEGs with the 7 lint yield QTL (XLSX 24 kb)

Supplementary Data 7. Confirmation of the predicted SNPs (XLSX 10 kb)

Supplementary Data 8. Marker loci associated with various yield and fiber quality traits (XLSX 10 kb)

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Man, W., Zhang, L., Li, X. et al. A comparative transcriptome analysis of two sets of backcross inbred lines differing in lint-yield derived from a Gossypium hirsutum × Gossypium barbadense population. Mol Genet Genomics 291, 1749–1767 (2016). https://doi.org/10.1007/s00438-016-1216-x

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