title: A comparative transcriptome analysis of two sets of backcross inbred lines differing in lint-yield derived from a Gossypium hirsutum × Gossypium barbadense population.
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.
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.
authors.forename: Wu
authors.initials: W
authors.lastname: Man
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.
authors.forename: Liyuan
authors.initials: L
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.
authors.forename: Xihua
authors.initials: X
authors.lastname: Li
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.|Wuyang A & F Bureau, Luohe, Henan, China.
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Xie
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.
authors.forename: Wenfeng
authors.initials: W
authors.lastname: Pei
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China. yujw@cricaas.com.cn.
authors.forename: Jiwen
authors.initials: J
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China. yu@cricaas.com.cn.
authors.forename: Shuxun
authors.initials: S
authors.lastname: Yu
authors.affiliation: Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA. jinzhang@nmsu.edu.
authors.forename: Jinfa
authors.initials: J
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics; D003433:Crosses, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D003368:Gossypium / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D018807:Polymorphism, Single-Stranded Conformational; D040641:Quantitative Trait Loci
chemical_list: D010940:Plant Proteins
keywords: Backcross inbred lines; Cotton yield; Differentially expressed genes; Microarray; Single nucleotide polymorphism