Fiber Quality In Upland Cotton Research Articles

Impacts of wide row spacings on yield and yield components of upland cotton (Gossypium hirsutum L.)

AbstractThis study quantifies the effects of wide row spacing on lint yield, yield components, and fiber quality of upland cotton (Gossypium hirsutum L.). An experiment was conducted in Tifton, GA in 2021 and 2022, where cotton was planted in six replications of 91‐, 122‐, 152‐, and 183‐cm row spacings. Following defoliation, 1.8 m was hand harvested from each plot, and boll density plant−1 and density ha−1 were determined for sympodial and monopodial branches. Additional measurements included fruit and lint yield distribution assessments and intra‐boll yield components including seed cotton weight boll−1, seed index, seed boll−1, lint weight seed−1, seed surface area (SSA), fiber density, and single fiber weight. Lint yield was reduced 20% in the 183‐cm row spacing compared to the 91‐cm row spacing. The 91‐cm rows had the lowest number of sympodial bolls plant−1 with 152‐ and 183‐cm rows demonstrating a 24%–28% increase in sympodial bolls plant−1. Sympodial bolls ha−1 were reduced 22% in the 183‐cm row spacing compared to the 91‐cm row spacing. There were no differences in bolls ha−1 or lint yield ha−1 with respect to monopodial growth. There were no differences in seed cotton weight boll−1, seeds boll−1, fiber density, single fiber weight, or turnout. Seed index and SSA were increased in the 183‐cm row spacing. Lint weight seed−1 was reduced in the 91‐cm row spacing.

Exploitation of heterotic effects in F1 hybrids for promoting earliness, yield components, and fiber quality of upland cotton (Gossypium hirsutum L.) genotypes

Exploitation of heterotic effects in F1 hybrids for promoting earliness, yield components, and fiber quality of upland cotton (Gossypium hirsutum L.) genotypes

Exogenous application of bio-stimulants and growth retardants improve nutrient absorption and fiber quality in upland cotton

BackgroundNatural and synthetic plant growth regulators are essential for plant health, likewise these regulators also play a role in increasing organic production productivity and improving quality and yield stability. In the present study, we have evaluated the effects of foliar applied plant growth regulators, i.e., moringa leaf extract (MLE) and mepiquat chloride (MC) alone and in combination MC and MLE on the conventional cotton cultivar (CIM 573) and transgenic one (CIM 598). The growth regulators were applied at the start of bloom, 45 and 90 days after blooming.ResultsThe application of MC and MLE at 90 days after blooming significantly improved the relative growth rate, net assimilation rate, the number of bolls per plant, and seed cotton yield. Likewise, the combined application of MLE and MC at 90 days after blooming significantly boosted the nitrogen uptake in locules, as well as the phosphorus and potassium uptake in the leaves of both cotton cultivars. The application of MLE alone has considerably improved the nitrogen uptake in leaves, and phosphorus and potassium contents in locules of Bt and conventional cotton cultivars. Similarly, Bt cotton treated with MLE at 90 days after blooming produced significantly higher ginning out turn and oil contents. Treatment in combination (MLE + MC) at 90 days after blooming produced considerably higher micronaire value, fiber strength, and staple length in conventional cultivar.ConclusionThe natural growth enhancer, MLE is a rich source of minerals and zeatin, improving the nutrient absorption and quality of cotton fiber in both conventional and Bt cotton cultivars.

An analysis of lncRNAs related to fiber quality and the discovery of their target genes in a Gossypium hirsutum line with Gossypium mustelinum introgression.

Analysis of fiber quality lncRNAs and their target genes from a pair of Gossypium mustelinum near-isogenic lines provide new prospects for improving the fiber quality of Upland cotton. Long noncoding RNAs (lncRNAs) are an important part of genome transcription and play roles in a wide range of biological processes in plants. In this research, a pair of near-isogenic cotton lines, namely, a Gossypium mustelinum introgression line (IL9) with outstanding fiber quality and its recurrent Upland cotton parent (PD94042), were used as the experimental materials. Cotton fibers were selected for lncRNA sequencing at 17 and 21days post-anthesis. A total of 2693 differentially expressed genes were identified. In total, 5841 lncRNAs were ultimately screened, from which 163 differentially expressed lncRNAs were identified. Target genes of the lncRNAs were predicted by two different methods: cis and trans. Some of the target genes were related to cell components, membrane components, plant hormone signal transduction and catalytic metabolism, and the results indicated that there might also be important effects on the development of fiber. Four differentially expressed target genes related to fiber quality (Gomus.D05G015100, Gomus.A05G281300, Gomus.A12G023400 and Gomus.A10G226800) were screened through gene function annotation, and the functions of these four genes were verified through virus-induced gene silencing (VIGS). Compared to the negative controls, plants in which any of these four genes were silenced showed significant reductions in fiber strength. In addition, the plants in which the Gomus.A12G023400 gene was silenced showed a significant reduction in fiber uniformity, whereas the plants in which Gomus.A05G281300 was silenced showed a significant increase in fiber fineness as measured via micronaire. Our results showed that these genes play different roles during fiber development, impacting fiber quality.

Investigating the Combining Ability of Yield and Fiber Quality in Upland Cotton (Gossypium hirsutum L.)

Investigating the Combining Ability of Yield and Fiber Quality in Upland Cotton (Gossypium hirsutum L.)

Genotypic and environmental contributions to lint yield, yield components, and fiber quality in upland cotton from Arkansas variety trials over a 19‐year period

AbstractLint yields and their underlying yield components can be substantially influenced by genotype and environment. Thus, the objectives of the current study were to quantify genotypic and environmental contributions to lint yield, yield components, and fiber quality in multi‐site variety trials conducted in Arkansas over a 19‐year period, to identify the traits most strongly associated with lint yield, and to quantify long‐term trends in the aforementioned traits. Annual assessments included lint yield, seeds per hectare (SPH), intra‐boll yield components, and fiber quality parameters. Production environment accounted for a higher percentage of all yield variability in 15 out of 19 years. However, four years were identified in which genotypic contributions were greater than environmental contributions. Genotype was a dominant driver of variability in lint percent, lint index, seed score, seed index, fibers per seed, fiber density, fiber length, strength, and uniformity. Production environment was the dominant driver of variability in SPH, and micronaire. Correlations between yield components and yield varied substantially from year to year, even when genotype was the primary yield driver. A regression function that utilized lint index and SPH was a stronger and more consistent indicator of genotypic variation in lint yield than any single yield component. Finally, long‐term trends show that lint percent has increased significantly over the past 19 years, whereas seed index has declined 19.6% for cotton varieties with the highest lint yields.

Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum.

Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties (sGK156 and 901-001) and were used here to investigate the source of high-quality related alleles. Based on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24,425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4,850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable quantitative trait loci (QTLs), we found 289 QTLs, of which 36 of them were stable QTLs and 18 were novel. Based on the transcriptome analysis for two parents and two RILs, 24,941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength (FS) QTLs, 320 DEGs were identified, suggesting that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence FS, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits.

Boron application influenced growth, yield and fiber quality of upland cotton (Gossipium hirsutum L.) under different irrigation regimes

Cotton is a major imperative cash crop crop globally including Pakistan. Among abiotic stresses, drought stress is critical that suppress plant growth, reduce crop production, low fiber quality and poor earnings for farmers. Nutrient deficiency is major factor resulting in poor crop production. Sufficient nutrient application has better capability to increase yield because it helps to plants to stand against adverse climatic conditions within the growing areas. Therefore, present study was conducted on evaluation of cultivars performance applying numerous irrigation systems and use of boron through different methods. Cultivar CIM-678 had maximum growth traits, allometry parameters and fiber quality attributes than CIM-602 which had minimum growth, allometry and fiber quality traits. Foliar application of boron and field capacity (75%) also increased plant growth, allometry and fiber traits. The interactive effects of cultivars, boron use and field capacity were improved the plant growth, yield, allometry parameter and fiber quality traits. Conclusively, CIM-678, boron foliar spray and field capacity (75%) improved the cotton crop production with excellent fiber quality traits. Keywords: BCR; Drought stress; Field capacity; Foliar spray http://dx.doi.org/10.19045/bspab.2021.100139

QTL mapping of agronomic and economic traits for four F2 populations of upland cotton

BackgroundUpland cotton (Gossypium hirsutum) accounts for more than 90% of the annual world cotton output because of its high yield potential. However, yield and fiber quality traits often show negative correlations. We constructed four F2 populations of upland cotton, using two normal lines (4133B and SGK9708) with high yield potential but moderate fiber quality and two introgression lines (Suyuan04–3 and J02–247) with superior fiber quality, and used them to investigate the genetic basis underlying complex traits such as yield and fiber quality in upland cotton. We also phenotyped eight agronomic and economic traits and mapped quantitative trait loci (QTLs).ResultsExtensive phenotype variations and transgressive segregation were found across the segregation populations. We constructed four genetic maps of 585.97 centiMorgan (cM), 752.45 cM, 752.45 cM, and 1 163.66 cM, one for each of the four F2 populations. Fifty QTLs were identified across the four populations (7 for plant height, 27 for fiber quality and 16 for yield). The same QTLs were identified in different populations, including qBW4 and qBW2, which were linked to a common simple sequence repeat (SSR) marker, NAU1255. A QTL cluster containing eight QTLs for six different traits was characterized on linkage group 9 of the 4133B × Suyuan04–3 population.ConclusionsThese findings will provide insights into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding.

The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton.

Cellulose synthases (CesAs) are multi-subunit enzymes found on the plasma membrane of plant cells and play a pivotal role in cellulose production. The cotton fiber is mainly composed of cellulose, and the genetic relationships between CesA genes and cotton fiber yield and quality are not fully understood. Through a phylogenetic analysis, the CesA gene family in diploid Gossypium arboreum and Gossypium raimondii, as well as tetraploid Gossypium hirsutum ('TM-1') and Gossypium barbadense ('Hai-7124' and '3-79'), was divided into 6 groups and 15 sub-groups, with each group containing two to five homologous genes. Most CesA genes in the four species are highly collinear. Among the five cotton genomes, 440 and 1929 single nucleotide polymorphisms (SNPs) in the CesA gene family were identified in exons and introns, respectively, including 174 SNPs resulting in amino acid changes. In total, 484 homeologous SNPs between the A and D genomes were identified in diploids, while 142 SNPs were detected between the two tetraploids, with 32 and 82 SNPs existing within G. hirsutum and G. barbadense, respectively. Additionally, 74 quantitative trait loci near 18 GhCesA genes were associated with fiber quality. One to four GhCesA genes were differentially expressed (DE) in ovules at 0 and 3days post anthesis (DPA) between two backcross inbred lines having different fiber lengths, but no DE genes were identified between these lines in developing fibers at 10 DPA. Twenty-seven SNPs in above DE CesA genes were detected among seven cotton lines, including one SNP in Ghi_A08G03061 that was detected in four G. hirsutum genotypes. This study provides the first comprehensive characterization of the cotton CesA gene family, which may play important roles in determining cotton fiber quality.

QTL controlling fiber quality traits under salt stress in upland cotton (Gossypium hirsutum L.)

Key messageQTL for fiber quality traits under salt stress discerned candidate genes controlling fatty acid metabolism.Salinity stress seriously affects plant growth and limits agricultural productivity of crop plants. To dissect the genetic basis of response to salinity stress, a recombinant inbred line population was developed to compare fiber quality in upland cotton (Gossypium hirsutum L.) under salt stress and normal conditions. Based on three datasets of (1) salt stress, (2) normal growth, and (3) the difference value between salt stress and normal conditions, 51, 70, and 53 QTL were mapped, respectively. Three QTL for fiber length (FL) (qFL-Chr1-1, qFL-Chr5-5, and qFL-Chr24-4) were detected under both salt and normal conditions and explained 4.26%, 9.38%, and 3.87% of average phenotypic variation, respectively. Seven genes within intervals of two stable QTL (qFL-Chr1-1 and qFL-Chr5-5) were highly expressed in lines with extreme long fiber. A total of 35 QTL clusters comprised of 107 QTL were located on 18 chromosomes and exhibited pleiotropic effects. Thereinto, two clusters were responsible for improving five fiber quality traits, and 6 influenced FL and fiber strength (FS). The QTL with positive effect for fiber length exhibited active effects on fatty acid synthesis and elongation, but the ones with negative effect played passive roles on fatty acid degradation under salt stress.

RNA-seq reveals hormone-regulated synthesis of non-cellulose polysaccharides associated with fiber strength in a single-chromosomal-fragment-substituted upland cotton line

Cotton fibers are the main raw materials of the textile industry. Exogenous superior fiber genes have been introduced into upland cotton to develop high-yield cultivars with excellent fiber quality. We used a single chromosomal segment on the chromosome A07 substitution line SL7, with high fiber strength, to investigate the molecular mechanism underlying its fiber quality. RNA-seq and KEGG analysis showed that 70 differentially expressed genes were enriched in plant hormone transduction pathways, including auxin, ethylene and abscisic acid, in fibers at 10 days post-anthesis (DPA). Among these, fiber-development related transcription factors MYB and NAC, including Gh_A11G0981 (MYB108), Gh_A03G0887 (NAC029), and Gh_A08G1691 (NAC021), were significantly upregulated in SL7, as were numerous cellulose synthase-like (CSL) genes involved in non-cellulose polysaccharide and cell wall synthesis. The hemicellulose content of SL7 was significantly higher than that of L22, an upland cotton cultivar. These results suggest that key genes in the introgressed chromosomal segment of SL7 regulate the expression of transcription-factor genes via hormone-transduction pathways, thereby inducing the expression of genes involved in secondary wall synthesis and ultimately improving fiber quality. This study has shed light on the molecular mechanism of fiber development and will contribute to the improvement of fiber quality of upland cotton by molecular breeding.

Transcriptome analysis reveals differences in the mechanisms of fiber initiation and elongation between long- and short-fiber cotton (Gossypium hirsutum L.) lines

BackgroundImproving the yield and fiber quality of upland cotton is a goal of plant breeders. However, increasing the yield and quality of cotton fibers is becoming more urgent. While the growing human population needs more cotton fiber, climate change is reducing the amount of land on which cotton can be planted, or making it difficult to ensure that water and other resources will be available in optimal quantities. The most logical means of improving yield and quality is understanding and manipulating the genes involved. Here, we used comparative transcriptomics to explore differences in gene expression between long- and short-fiber cotton lines to identify candidate genes useful for cotton improvement.ResultsLight and electron microscopy revealed that the initial fiber density was significantly greater in our short-fiber group (SFG) than in our long-fiber group (LFG). Compared with the SFG fibers, the LFG fibers were longer at all developmental stages. Comparison of the LFG and SFG transcriptomes revealed a total of 3538 differentially expressed genes (DEGs). Notably, at all three developmental stages examined, two expression patterns, consistently downregulated (profile 0) and consistently upregulated (profile 7), were identified, and both were significantly enriched in the SFG and LFG. Twenty-two DEGs known to be involved in fiber initiation were detected in profile 0, while 31 DEGs involved in fiber elongation were detected in profile 7. Functional annotation suggested that these DEGs, which included ERF1, TUA2, TUB1, and PER64, affect fiber elongation by participating in the ethylene response, microtubule synthesis, and/or the peroxidase (POD) catalytic pathway. qRT-PCR was used to confirm the RNA sequencing results for select genes.ConclusionsA comparison of SFG and LFG transcription profiles revealed modest but important differences in gene expression between the groups. Notably, our results confirm those of previous studies suggesting that genes involved in ethylene, tubulin, and POD pathways play important roles in fiber development. The 22 consistently downregulated DEGs involved in fiber initiation and the 31 consistently upregulated genes involved in fiber elongation are seemingly good candidate genes for improving fiber initiation and elongation in cotton.

Transcriptome and QTL analyses reveal candidate genes for fiber quality in Upland cotton

With increasing demand for high-quality cotton, it is desirable to identify genes involved in fiber development for molecular improvement of cotton. In this study, 780 differentially expressed genes (DEGs) were identified in developing fibers at 10 days post-anthesis (DPA) in Gossypium hirsutum acc. DH962 and G. hirsutum cv. Jimian 5 using RNA-seq. Of 15 stable QTL for fiber quality identified in the same two parents in previous studies, 4, 3, 6, 1, and 1 QTL were associated with fiber length (FL), fiber strength (FS), micronaire (MIC), fiber elongation (FE) and fiber length uniformity ratio (FU), respectively. Integration of DEGs and QTL allowed the identification of 31 genes in 9 QTL regions, of which 25 were highly expressed in fibers based on the transcriptome datasets and 9 were preferentially expressed in different stages of fiber development. Gh_A01G0453 (GhDTX19), Gh_D07G1581 and Gh_D04G0942 were expressed specifically in 5 and 10 DPA fibers, with Gh_D04G0942 showing low expression in other tissues except pistil. Gh_D07G1799 (GhGAUT9), Gh_D11G0326 (GhVPS29), Gh_D11G0333 (GhTCP14), and Gh_D11G0334 (GhNRP2) were preferentially expressed in 5 or 10 DPA fibers; Gh_A01G0397 (GhABCG10) and Gh_D07G1744 were expressed specifically in 20 and 25 DPA fibers. These results suggest candidate genes for molecular improvement of cotton fiber quality.

Identifying Functional Genes Influencing Gossypium hirsutum Fiber Quality.

Fiber quality is an important economic index and a major breeding goal in cotton, but direct phenotypic selection is often hindered due to environmental influences and linkage with yield traits. A genome-wide association study (GWAS) is a powerful tool to identify genes associated with phenotypic traits. In this study, we identified fiber quality genes in upland cotton (Gossypium hirsutum L.) using GWAS based on a high-density CottonSNP80K array and multiple environment tests. A total of 30 and 23 significant single nucleotide polymorphisms (SNPs) associated with five fiber quality traits were identified across the 408 cotton accessions in six environments and the best linear unbiased predictions, respectively. Among these SNPs, seven loci were the same, and 128 candidate genes were predicted in a 1-Mb region (±500 kb of the peak SNP). Furthermore, two major genome regions (GR1 and GR2) associated with multiple fiber qualities in multiple environments on chromosomes A07 and A13 were identified, and within them, 22 candidate genes were annotated. Of these, 11 genes were expressed [log2(1 + FPKM)>1] in the fiber development stages (5, 10, 20, and 25 dpa) using RNA-Seq. This study provides fundamental insight relevant to identification of genes associated with fiber quality and will accelerate future efforts toward improving fiber quality of upland cotton.

Single-Locus and Multi-Locus Genome-Wide Association Studies in the Genetic Dissection of Fiber Quality Traits in Upland Cotton (Gossypium hirsutum L.).

A major breeding target in Upland cotton (Gossypium hirsutum L.) is to improve the fiber quality. To address this issue, 169 diverse accessions, genotyped by 53,848 high-quality single-nucleotide polymorphisms (SNPs) and phenotyped in four environments, were used to conduct genome-wide association studies (GWASs) for fiber quality traits using three single-locus and three multi-locus models. As a result, 342 quantitative trait nucleotides (QTNs) controlling fiber quality traits were detected. Of the 342 QTNs, 84 were simultaneously detected in at least two environments or by at least two models, which include 29 for fiber length, 22 for fiber strength, 11 for fiber micronaire, 12 for fiber uniformity, and 10 for fiber elongation. Meanwhile, nine QTNs with 10% greater sizes (R2) were simultaneously detected in at least two environments and between single- and multi-locus models, which include TM80185 (D13) for fiber length, TM1386 (A1) and TM14462 (A6) for fiber strength, TM18616 (A7), TM54735 (D3), and TM79518 (D12) for fiber micronaire, TM77489 (D12) and TM81448 (D13) for fiber uniformity, and TM47772 (D1) for fiber elongation. This indicates the possibility of marker-assisted selection in future breeding programs. Among 455 genes within the linkage disequilibrium regions of the nine QTNs, 113 are potential candidate genes and four are promising candidate genes. These findings reveal the genetic control underlying fiber quality traits and provide insights into possible genetic improvements in Upland cotton fiber quality.

SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population.

The quality of fiber is significant in the upland cotton industry. As complex quantitative traits, fiber quality traits are worth studying at a genetic level. To investigate the genetic architecture of fiber quality traits, we conducted an association analysis using a multi-parent advanced generation inter-cross (MAGIC) population developed from eight parents and comprised of 960 lines. The reliable phenotypic data for six major fiber traits of the MAGIC population were collected from five environments in three locations. Phenotypic analysis showed that the MAGIC lines have a wider variation amplitude and coefficient than the founders. A total of 284 polymorphic SSR markers among eight parents screened from a high-density genetic map were used to genotype the MAGIC population. The MAGIC population showed abundant genetic variation and fast linkage disequilibrium (LD) decay (0.76cM, r2 > 0.1), which revealed the advantages of high efficiency and power in QTL exploration. Association mapping via a mixed linear model identified 52 significant loci associated with six fiber quality traits; 14 of them were mapped in reported QTL regions with fiber-related or other agronomic traits. Nine markers demonstrated the pleiotropism that controls more than two fiber traits. Furthermore, two SSR markers, BNL1231 and BNL3452, were authenticated as hotspots that were mapped with multi-traits. In addition, we provided candidate regions and screened six candidate genes for identified loci according to the LD decay distance. Our results provide valuable QTL for further genetic mapping and will facilitate marker-based breeding for fiber quality in cotton.

Registration of Two CS‐B17‐derived Upland Cotton Recombinant Inbred Lines with Improved Fiber Micronaire

A population of 50 chromosome‐specific cotton (Gossypium hirsutum L.) recombinant inbred lines (RILs), CS‐B17 RILs, was developed by inbreeding an F1 hybrid between ‘TM‐1’, the genetic standard line of upland cotton (G. hirsutum), and CS‐B17, a formally released interspecific chromosome substitution line. The parents, CS‐B17 and TM‐1, are genetically similar for all chromosome pairs except chromosome 17, which in CS‐B17 was replaced by chromosome 17 of 3‐79 (G. barbadense L.). Two CS‐B17 RILs, CS‐B17‐RIL‐59 (Reg. No. GP‐1021, PI 677340) and CS‐B17‐RIL‐98 (Reg. No. GP‐1022, PI 677342), were selected and released on the basis of their improved fiber quality traits, especially their favorable low micronaire values of 3.96 and 3.86, respectively, compared with the commercial lines ‘DP 393’ and ‘PHY 370 WR’, which had micronaire values of 4.52 and 4.58, respectively. However, the agronomic traits of the commercial lines were better than the released CS‐B17 RILs. Fiber with a micronaire value in the range of 3.7 to 4.2 is considered as the base range in the textile market, whereas US‐produced cotton averaged 4.40 over the past decade. These germplasm lines may provide genetic variation from G. barbadense that can be used to enhance cotton fiber quality of upland cotton.

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

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.

Registration of Cotton Germplasm Line, MD 10‐5

MD 10‐5 (Reg. No. GP‐999, PI 675077) is a noncommercial breeding line of cotton (Gossypium hirsutum L.) released by the USDA‐ARS at Stoneville, MS, in 2015. MD 10‐5 was selected in F5 progenies from a cross between MD 15 (PI 642769) and JJ 1145ne. MD 10‐5 has a desirable combination between lint yield and fiber properties, especially fiber strength. It produces lint yield higher than or comparable to the high‐yielding commercial cultivars and possesses fiber strength higher than or close to noncommercial germplasm lines known for high fiber quality. Other fiber properties including fiber length, elongation, uniformity, micronaire, and yarn tenacity were generally comparable to the high fiber quality checks. MD 10‐5 was mainly selected and evaluated in the mid‐south United States, but it was also evaluated across 14 locations in the US Cotton Belt. It displays a broad adaptation to different environments in the US cotton production regions. MD 10‐5 provides opportunities for cotton breeders to improve both lint yield and fiber quality in upland cotton.