Large‐scale resource development in Gossypium hirsutum L. by 454 sequencing of genic‐enriched libraries from six diverse genotypes

Abstract

SummaryThe sequence information has been proved to be an essential genomic resource in case of crop plants for their genetic improvement and better utilization by humans. To dissect the Gossypium hirsutum genome for large-scale development of genomic resources, we adopted hypomethylated restriction-based genomic enrichment strategy to sequence six diverse genotypes. Approximately 5.2-Gb data (more than 18.36 million reads) was generated which, after assembly, represents nearly 1.27-Gb genomic sequences. We predicted a total of 93 363 gene models (21 399 full length) and identified 35 923 gene models which were validated against already sequenced plant genomes. A total of 1093 transcription factor-encoding genes, 3135 promoter sequences and 78 miRNA (including 17 newly identified in Gossypium) were predicted. We identified significant no. of molecular markers including 47 093 novel simple sequence repeats and 66 364 novel single nucleotide polymorphisms. In addition, we developed NBRIComprehensive Cotton Genomics database, a web resource to provide access of cotton-related genomic resources developed at NBRI. This study contributes considerable amount of genomic resources and suggests a potential role of genic-enriched sequencing in genomic resource development for orphan crop plants.

A Long‐Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery

“…The G. hirsutum transcriptome assembly presented here consists of 72,450 nonredundant contigs. The average length of contigs (976 nt) was very close to that of a recently reported transcriptome assembly of cotton (Rai et al, 2013). Despite availability of genome sequences of G. raimondii (D 5 ) (Paterson et al, 2012) and G. arboreum (A 2 ) (Li et al, 2014), the transcriptome assembly of G. hirsutum is important in many aspects.…”

“…Within a subset of Class I SNPs the validation rate was 72%, a high validation rates for intraspecific G. hirsutum SNPs. We used one pooled Roche 454 cDNA library for transcriptome assembly with 1.5 million reads compared with another study (Rai et al, 2013) in which they used two genomic libraries of each six diverse G. hirsutum genotypes that resulted in generating >14 million Roche 454 reads. Having a larger dataset, Rai et al (2013) were able to identify over 66,000 nonredundant SNPs among the six lines that they used within the genic and nongenic sequences, though the validation rate was not specified (Zhu et al, 2014).…”

“…However, two genome sequence assemblies of the diploid relative cotton G. raimondii (D5) have been released independently by two research groups (Paterson et al, 2012; Wang et al, 2012), and an A2 genome sequence assembly for G. arboreum was recently released publicly (Li et al, 2014). These genomic resources have fostered rapid progress in Gossypium genomics, including several recently reported large‐scale SNP development efforts (Byers et al, 2012; Gore et al, 2012; Hulse‐Kemp et al, 2014; Islam et al, 2015; Lacape et al, 2012; Rai et al, 2013; Zhu et al, 2014). A number of these SNP resources were contributed to an international consortium for possible inclusion in a SNP chip, which was released in early 2014 and consists of high‐quality high‐density SNP arrays, each containing ∼63,000 Infinium assays (http://www.illumina.com/applications/agriculture/consortia.html; Hulse‐Kemp, 2014).…”

Genome-Wide SNP Linkage Mapping and QTL Analysis for Fiber Quality and Yield Traits in the Upland Cotton Recombinant Inbred Lines Population

“…The array, consisted of 63,058 SNPs, were derived from published literatures (Van Deynze et al, 2009; Byers et al, 2012; Lacape et al, 2012; Rai et al, 2013). Candidate SNPs suitable for further analysis were identified as follows: (1) SNPs were filtered by excluding those with monomorphic markers or with poor quality data; (2) SNPs which the parental genotypes were inconsistent with progeny genotypic ratios or parental genotypes data had missing information were removed from the dataset; (3) SNPs of 188 RILs with missing values more than 40% were removed.…”

Genome mapping and molecular markers identification for yield, yield component and fibre quality traits in tetraploid cotton

“…The large number of SNP markers detected in different cotton species (Byers, Harker, Yourstone, Maughan, & Udall, ; Van Deynze et al, ; Gore et al, ; Hulse‐Kemp, Ashrafi, et al, ; Hulse‐Kemp et al, ; Islam, Thyssen, Jenkins, & Fang, ; Lacape et al, ; Rai et al, ; Zhu, Spriggs, Taylor, Llewellyn, & Wilson, ) have helped the cotton researchers in genome‐based identification and mapping of QTL. Till now, only a few mapping studies in cotton have been based on SNP markers (Gore et al, ; Kumar et al, ; Li et al, ; Yu et al, ; Zhang et al, ).…”