QTL mapping for agronomic and fibre traits using two interspecific chromosome substitution lines of Upland cotton

Luan, Mingbao; Guo, Xiuping; Zhang, Y.; Yao, Jinbo; Chen, W.

doi:10.1111/j.1439-0523.2009.01650.x

Cited by 20 publications

(9 citation statements)

References 38 publications

(21 reference statements)

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“…Most QTL reports in cotton have related to fiber quality characteristics (Shen et al, 2006;Rong et al, 2007;Qin et al, 2008;Luan et al, 2009;Wu et al, 2009;Lacape et al, 2010), while only a few reports have considered other traits, such as yieldrelated traits (Ulloa and Meredith, 2000;Shen et al, 2007;Wang et al, 2007;Liu et al, 2011). We located 166 QTLs for 27 different traits related to plant morphology, flowering phenology, and yield components.…”

Section: Discussionmentioning

confidence: 99%

“…Molecular dissection of traits through mapping of quantitative trait loci, QTL, in cotton has concentrated mostly on fiber quality parameters (Shen et al, 2006;Rong et al, 2007;Qin et al, 2008;Luan et al, 2009;Lacape et al, 2010), including a recent QTL metaanalysis integrating QTL data from the same interspecific Gh × Gb RIL population reported here with QTL data from the literature (Lacape et al, 2010). Reports for QTLs for yield or yield-related traits have been scarce, mostly based upon intra-hirsutum segregating populations and were only poorly documented in terms of consistency of QTL detection between different studies (Ulloa and Meredith, 2000;Shen et al, 2007;Wang et al, 2007;Wu et al, 2009;Liu et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

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Mapping QTLs for traits related to phenology, morphology and yield components in an inter-specific Gossypium hirsutum×G. barbadense cotton RIL population

Lacape

Gawrysiak

Cao

et al. 2013

Field Crops Research

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Two major cultivated cotton species, Gossypium hirsutum (Gh) and G. barbadense (Gb) contribute to the bulk of cotton fiber production worldwide (95%). These species are largely inter-fertile and each displays a series of distinctive characteristics in terms of numerous botanical features and, more importantly, in their agronomic performance, adaptability and overall fiber quality. A recombinant inbred line (RIL) population derived from an inter-specific cross between Gh and Gb, used previously for QTL mapping of fiber quality characteristics, has also been evaluated over 6 sites and 2 years for various plant morphological, phenological and yield component traits. A total of 27 traits were assessed across a varying number of locations (up to 6 locations, in Australia, USA, Brazil, Cameroon, Belgium and France) and years, representing up to 10 different combinations. Variability in many of these traits was observed among the RILs and they frequently showed transgression. One hundred and sixty six significant QTLs, covering the 27 traits, were detected by composite interval mapping when using individual datasets. Cases of confirmation of localizations of individual QTLs from different data sets were detected in 27 instances, indicating that the 166 individual QTLs in this study could be represented by a maximum of 121 chromosome positions. QTL were shared between traits related to hairiness (22 individual QTLs), plant morphology of vegetative (29 QTLs) and reproductive (37 QTLs) parts, phenology (17 QTLs), and yield-related traits (61 QTLs). This is the first report of QTL mapping in cotton for various within-boll yield-related traits assessed on a per-seed basis, including fiber mass per unit of seed surface area (5 QTLs), calculated number of fibers per seed (2 QTLs) or per unit of seed surface area (1 QTL). This report confirms the importance of considering such basic yield components in selection for better yielding cotton varieties.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mapping QTLs for traits related to phenology, morphology and yield components in an inter-specific Gossypium hirsutum×G. barbadense cotton RIL population

Lacape

Gawrysiak

Cao

et al. 2013

Field Crops Research

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“…A quantitative trait locus (QTL) mapping approach can be informative for studying quantitative inheritance, for detecting genomic regions associated with morphological, yield and fiber quality traits, and for identifying molecular markers linked to the genes conferring the phenotypic expression of the important traits (Draye et al 2005;Kohel et al 2001;Lacape et al 2005;Luan et al 2009;Park et al 2005;Shen et al 2005;Song and Zhang 2009;Ulloa et al 2007;Zhu et al 2011). Molecular markers located in the cotton genome are used to address fundamental questions regarding the genetic factors for these traits (Lacape et al 2010(Lacape et al , 2013Mohan et al 1997).…”

Section: Introductionmentioning

confidence: 97%

Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. × G. barbadense L.) RIL population

Ulloa²,

Hoffman

et al. 2014

Mol Genet Genomics

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A quantitative trait locus (QTL) mapping was conducted to better understand the genetic control of plant architecture (PA), yield components (YC), and fiber properties (FP) in the two cultivated tetraploid species of cotton (Gossypium hirsutum L. and G. barbadense L.). One hundred and fifty-nine genomic regions were identified on a saturated genetic map of more than 2,500 SSR and SNP markers, constructed with an interspecific recombinant inbred line (RIL) population derived from the genetic standards of the respective cotton species (G. hirsutum acc. TM-1 × G. barbadense acc. 3-79). Using the single nonparametric and MQM QTL model mapping procedures, we detected 428 putative loci in the 159 genomic regions that confer 24 cotton traits in three diverse production environments [College Station F&B Road (FB), TX; Brazos Bottom (BB), TX; and Shafter (SH), CA]. These putative QTL loci included 25 loci for PA, 60 for YC, and 343 for FP, of which 3, 12, and 60, respectively, were strongly associated with the traits (LOD score ≥ 3.0). Approximately 17.7 % of the PA putative QTL, 32.9 % of the YC QTL, and 48.3 % of the FP QTL had trait associations under multiple environments. The At subgenome (chromosomes 1-13) contributed 72.7 % of loci for PA, 46.2 % for YC, and 50.4 % for FP while the Dt subgenome (chromosomes 14-26) contributed 27.3 % of loci for PA, 53.8 % for YC, and 49.6 % for FP. The data obtained from this study augment prior evidence of QTL clusters or gene islands for specific traits or biological functions existing in several non-homoeologous cotton chromosomes. DNA markers identified in the 159 genomic regions will facilitate further dissection of genetic factors underlying these important traits and marker-assisted selection in cotton.

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“…When combing the information of maps form Luan et al. () and Blenda et al. (), the substituted fragment might be in the interval of 61.1 cM (TMB2938) ‐126.4 cM (JESPR156) of consensus map from Blenda et al.…”

Section: Discussionmentioning

confidence: 99%

The development of specific SNP markers for chromosome 14 in cotton using next‐generation sequencing

et al. 2014

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Lacking of reference genome sequence for the development of stable molecular markers for specific chromosomes (intervals) remains to be a challenge in cotton, which was a necessary step in fine mapping of gene (QTL). In this study, the feasibility of development of single-nucleotide polymorphism (SNP) markers between CS-B14Sh (a substitution line for short arm of Chromosome 14) and TM-1 (the recurrent parent) was explored using next-generation sequencing (NGS) based on reduced representation libraries (RRLs). High-quality genome sequences, representing about 7.1%, 8.8% and 10.4% of the tetraploid cotton genome, were generated for TM-1, 3-79 (the donor parent) and CS-B14Sh, respectively. A total of 397 putative SNP markers were detected between CS-B14Sh and TM-1, and most (358) of them were also detected between TM-1 and 3-79. Allele-specific PCR method was used for validation of 40 SNP markers, and 27 of them showed polymorphism between TM-1 and CS-B14Sh, and a linkage group comprising of 25 SNP markers and five SSR markers was constructed. The order of SNP markers agreed well with the position of them on Chr05 of D genome, which further approved the truth of SNPs detected. The results suggested that the development of SNP markers in specific genome region using NGS was efficient in substitution or near-isogenic lines.

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QTL mapping for agronomic and fibre traits using two interspecific chromosome substitution lines of Upland cotton

Cited by 20 publications

References 38 publications

Mapping QTLs for traits related to phenology, morphology and yield components in an inter-specific Gossypium hirsutum×G. barbadense cotton RIL population

Mapping QTLs for traits related to phenology, morphology and yield components in an inter-specific Gossypium hirsutum×G. barbadense cotton RIL population

Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. × G. barbadense L.) RIL population

The development of specific SNP markers for chromosome 14 in cotton using next‐generation sequencing

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