Registration of RMUP‐C5, a Random Mated Population of Upland Cotton Germplasm

Jenkins, Johnie N.; McCarty, Jack C.; Gutiérrez, Osman A.; Hayes, R. W.; Bowman, Daryl T.; Watson, C. E.; Jones, Douglas T.

doi:10.3198/jpr2008.02.0080crg

Cited by 34 publications

(31 citation statements)

References 14 publications

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“…1 and Additional file 2) [9]. The effectiveness of random-mating and its consequence on structure of this population was evaluated using 6039 SNP and 223 SSR markers.…”

Section: Resultsmentioning

confidence: 99%

“…1. The details of the population development were previously described by [4, 9, 27]. In brief, a half-diallel crossing scheme between 11 parents were followed to produce 55 F 1 in 2002.…”

Section: Methodsmentioning

confidence: 99%

“…A multi-parent advanced generation inter-cross (MAGIC) strategy has been anticipated to have higher genetic diversity, smaller haplotype blocks, higher recombination and better mapping resolution [8]. Thus, a MAGIC population in cotton has a better chance to break the negative linkage between yield and fiber quality [9]. Very recently, use of a MAGIC population to identify QTL has become a new approach, thanks to the advancement of next generation sequencing (NGS) techniques and novel statistical and bioinformatics tools to analyze large data sets.…”

Section: Introductionmentioning

confidence: 99%

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A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

et al. 2016

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BackgroundCotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders’ ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP). Genotyping a MAGIC population using GBS technologies will enable us to identify marker-trait associations with high resolution.ResultsAn Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By employing a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits [short fiber content (SFC), strength (STR), length (UHM) and uniformity (UI)] on chromosome A07. We further identified candidate genes related to fiber quality attributes in this region. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars.ConclusionUsing GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection or genomic selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3249-2) contains supplementary material, which is available to authorized users.

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“…1 and Additional file 2) [9]. The effectiveness of random-mating and its consequence on structure of this population was evaluated using 6039 SNP and 223 SSR markers.…”

Section: Resultsmentioning

confidence: 99%

“…1. The details of the population development were previously described by [4, 9, 27]. In brief, a half-diallel crossing scheme between 11 parents were followed to produce 55 F 1 in 2002.…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

et al. 2016

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“…Random mating procedures have provided an important methodology to break undesirable associations and to form new combinations in several crop plants, including tobacco [9], sorghum [10], soybean [11], and oats [12]. Random mating has previously been shown to reduce correlations between traits in cotton as well [8, 13–15]. Random mating requires a considerable expenditure of time and energy.…”

Section: Introductionmentioning

confidence: 99%

Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.)

et al. 2014

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BackgroundUpland cotton (Gossypium hirsutum L.) accounts for about 95% of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between yield and fiber quality is an obstacle for cotton improvement. Random-mating provides a potential methodology to break this correlation. The suite of fiber quality traits that affect the yarn quality includes the length, strength, maturity, fineness, elongation, uniformity and color. Identification of stable fiber quantitative trait loci (QTL) in Upland cotton is essential in order to improve cotton cultivars with superior quality using marker-assisted selection (MAS) strategy.ResultsUsing 11 diverse Upland cotton cultivars as parents, a random-mated recombinant inbred (RI) population consisting of 550 RI lines was developed after 6 cycles of random-mating and 6 generations of self-pollination. The 550 RILs were planted in triplicates for two years in Mississippi State, MS, USA to obtain fiber quality data. After screening 15538 simple sequence repeat (SSR) markers, 2132 were polymorphic among the 11 parents. One thousand five hundred eighty-two markers covering 83% of cotton genome were used to genotype 275 RILs (Set 1). The marker-trait associations were analyzed using the software program TASSEL. At p < 0.01, 131 fiber QTLs and 37 QTL clusters were identified. These QTLs were responsible for the combined phenotypic variance ranging from 62.3% for short fiber content to 82.8% for elongation. The other 275 RILs (Set 2) were analyzed using a subset of 270 SSR markers, and the QTLs were confirmed. Two major QTL clusters were observed on chromosomes 7 and 16. Comparison of these 131 QTLs with the previously published QTLs indicated that 77 were identified before, and 54 appeared novel.ConclusionsThe 11 parents used in this study represent a diverse genetic pool of the US cultivated cotton, and 10 of them were elite commercial cultivars. The fiber QTLs, especially QTL clusters reported herein can be readily implemented in a cotton breeding program to improve fiber quality via MAS strategy. The consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying fiber development.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-397) contains supplementary material, which is available to authorized users.

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“…These results are at odds with results from studies of agronomically elite germplasm that often report negative relationships between yield components and fiber quality. Prior studies by Jenkins et al (2008) also reported changes in correlations among traits after six cycles of random mating in a cotton population. The process of random mating, whether using bulked pollen (Jenkins et al, 2008) or male‐sterile methodology, may change genetic relationships by reconfiguring epistatic interactions.…”

Section: Characteristicsmentioning

confidence: 87%

Registration of Four Diverse Random-Mated Cotton Germplasm Populations

Hinze

Kohel

Campbell³

et al. 2013

Journal of Plant Registrations

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Dwarf GP (Reg. No. GP‐967; PI 669119), Fiber GP (Reg. No. GP‐968; PI 669120), Glandless GP (Reg. No. GP‐969; PI 669121), and Race GP (Reg. No. GP‐970; PI 669122) are four unique upland cotton (Gossypium hirsutum L.) germplasm populations (GP) released by the USDA–ARS. Dwarf GP is a four‐parent, narrow‐based population developed to incorporate dwarfing genes into nondwarf genetic backgrounds. The remaining three populations are broad‐based, complex populations. Fiber GP (24 parents) was developed to include potential sources of variation that would improve fiber length and strength. At the time these populations were developed, a viable glandless seed industry existed, and Glandless GP (22 parents) incorporated glandless germplasm from public and private breeders. Race GP (42 parents) was developed to obtain new genetic recombination events among a set of primitive race stock parents. These populations were created to recombine the variability from multiple parents into a single source from which selection can be initiated. Glandless GP was formed by random mating for nine cycles using a bulked pollen methodology. Dwarf GP, Fiber GP, and Race GP were formed by random mating for one cycle using a bulked pollen methodology followed by eight cycles using a male sterile. These populations possess trait specific and non‐trait specific genetic diversity resulting from multiple generations of recombination and, therefore, present breeders with useful tools for improvement of elite germplasm.

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Registration of RMUP‐C5, a Random Mated Population of Upland Cotton Germplasm

Cited by 34 publications

References 14 publications

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.)

Registration of Four Diverse Random-Mated Cotton Germplasm Populations

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