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Within-sample variation in cotton fiber length is a major factor influencing the production and quality of yarns. The textile industry has been searching for approaches of improving the long fiber fraction and minimizing the short fiber fraction within a cotton sample to produce superior fiber and yarn quality. USTER® High Volume Instrument (HVI) has been widely used for a rapid assessment of cotton fiber length traits from a fiber bundle. However, its effectiveness for genetic studies has been questioned due to the indirect estimations of the cotton fiber traits that cannot be measured from a fiber bundle. To overcome the limits of the HVI fiber length traits, we utilized the Advanced Fiber Information System (AFIS) measuring fiber length traits directly from individual fibers based on weight or number. Comparative fiber length analyses showed AFIS provided higher sensitivity in detecting the fiber length variations within and among cotton samples than HVI. The weight-based AFIS length traits were strongly correlated with the corresponding HVI lengths, whereas the number-based AFIS mean length showed a relatively weaker correlation with the HVI lengths. Integrations of the weight based-length traits with genome-wide association studies (GWAS) enabled classifying the QTLs specifically associated with long, mean, or short fiber length traits and identified a false positive associated with the indirectly estimated HVI short fiber trait. Unlike the weight based-AFIS length traits, the number-based AFIS length trait did not show a negative correlation with a weight related-HVI property, and identified a single QTL that was not detected by the corresponding HVI trait. These results suggested that integrating the AFIS method with GWAS helped discoveries of the genome loci involved in the within-sample variation in cotton fiber length and characterizations of the fiber length QTLs. [ABSTRACT FROM AUTHOR]

The genetic base for upland cotton (Gossypium hirsutum L.) is narrow for the economically important fiber traits of strength and length. We developed random mated population RMUP‐C5 from 11 parental lines and released seed in 2008. We have now developed 550 recombinant inbred lines (RILs) from this population and evaluated them for fiber properties in eight environments. We report the development and release of seven RILs with improved fiber strength and/or upper half mean length: MS‐RIL‐009 (Reg. no. GP‐1100, PI 698460), MS‐RIL‐037 (Reg. no. GP‐1101, PI 698461), MS‐RIL‐204 (Reg. no. GP‐1102, PI 698462), MS‐RIL‐219 (Reg no. GP‐1103, PI 698463), MS‐RIL‐282 (Reg. no. GP‐1104, PI 698464), MS‐RIL‐303 (Reg. no. GP‐1105, PI 698465), and MS‐RIL‐490 (Reg. no. GP‐1106, PI 698466). Fiber strength and length for the seven lines are as follows: MS‐RIL 009 (384, 30.0), MS‐RIL 037 (369, 31.3), MS‐RIL‐204 (333, 32.5), MS‐RIL‐219 (345, 31.8), MS‐RIL‐282 (295, 31.4), MS‐RIL‐303 (379, 31.4) and MS‐RIL‐490 (318, 33.0), kN m kg–1 and mm, respectively. Fibers of MS‐RILS 037, 219, and 303 are significantly stronger and longer, fibers of 009 are significantly stronger, and fibers of 204, 282, and 490 are significantly longer than fibers of 'Acala Ultima' or 'Fibermax 966', the parental lines with the strongest (326–334 kN m kg–1) and longest (29.3–30.0 mm) fibers. MS‐RIL‐009, MS‐RIL‐037, MS‐RIL‐219, and MS‐RIL‐303 are homozygous for favorable alleles at the A07 strength quantitative trait locus (QTL). All lines except MS‐RIL‐009 are homozygous for favorable alleles at the D11 length QTL. Core Ideas: Increased cotton fiber strength and length are needed for high‐speed spinning processes.Random mating followed by development of RIL recombines alleles into useful breeding lines.MS‐RIL‐037, 219, and 303 have significantly stronger and longer fiber than the best parent.MS‐RIL‐204, 282, and 490 have significantly longer fiber than the best parent.MS‐RIL‐009 has significantly stronger fiber than the best parent. [ABSTRACT FROM AUTHOR]

Abstract Background Cotton (Gossypium spp.) is produced in over 30 countries and represents the most important natural fiber in the world. One of the primary factors affecting both the quantity and quality of cotton production is water. A major facilitator of water movement through cell membranes of cotton and other plants are the aquaporin proteins. Aquaporin proteins are present as diverse forms in plants, where they function as transport systems for water and other small molecules. The plant aquaporins belong to the large major intrinsic protein (MIP) family. In higher plants, they consist of five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). Although a great deal is known about aquaporins in plants, very little is known in cotton. Results From a molecular cloning effort, together with a bioinformatic homology search, 71 upland cotton (G. hirsutum) aquaporin genes were identified. The cotton aquaporins consist of 28 PIP and 23 TIP members with high sequence similarity. We also identified 12 NIP and 7 SIP members that showed more divergence. In addition, one XIP member was identified that formed a distinct 5th subfamily. To explore the physiological roles of these aquaporin genes in cotton, expression analyses were performed for a select set of aquaporin genes from each subfamily using semi-quantitative reverse transcription (RT)-PCR. Our results suggest that many cotton aquaporin genes have high sequence similarity and diverse roles as evidenced by analysis of sequences and their expression. Conclusion This study presents a comprehensive identification of 71 cotton aquaporin genes. Phylogenetic analysis of amino acid sequences divided the large and highly similar multi-gene family into the known 5 aquaporin subfamilies. Together with expression and bioinformatic analyses, our results support the idea that the genes identified in this study represent an important genetic resource providing potential targets to modify the water use properties of cotton.

In this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System (BIMS), a free, secure and online breeding management system that allows breeders to store, manage, archive and analyze their private breeding data. BIMS is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. BIMS incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. BIMS comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium. Database URLs: (https://www.rosaceae.org/), (https://www.cottongen.org/), (https://www.citrusgenomedb.org/), (https://www.pulsedb.org/) and (https://www.vaccinium.org/) [ABSTRACT FROM AUTHOR]

Determination of an efficient number of testing locations in multiple-location tests for cotton (Gossypium hirsutum L.) fiber quality can allow removal of unnecessary locations while maintaining the statistical power in detection of genotype (g) by environment (e) interactions. Fiber quality data from Regional High-Quality (RHQ) tests from 2011 to 2016 were used to determine an ef- ficient number of locations in the tests for fiber quality and relationships among locations for their representativeness and ability to discriminate among genotypes. Covariance parameters of g, location (l), and gl in the original RHQ tests were estimated in a random model. The simulating data with varying number of locations omitted from the original tests were created by performing 100 unique simulations. When locations were reduced to five, the standard deviations (std) of gl increased from 18 to 37% compared to the original tests. Further reduction of locations to four or less increased std of gl from 30 to 217% compared to the original tests. Therefore, five locations were determined to be an efficient number of locations in tests for fiber quality. The discriminating ability and representativeness of the eight locations for fiber properties were calculated as their distances to an "ideal environment", which was designed as a center in GGE biplot graphs for representativeness and discriminating ability. The relationships among locations were different across years. However, by averaging the distances across testing years, the locations of Stoneville, MS; Keiser, AR; Lubbock, TX; and College Station, TX were identified as the most representative testing sites for fiber properties. [ABSTRACT FROM AUTHOR]

Competition with manmade fibers has increased focus on upland cotton (Gossypium hirsutum L.) fiber quality, especially upper half mean length (FL), for industry stakeholders and breeders. The purpose of this study was to characterize the effect of qFL‐Chr.25, a quantitative trait locus (QTL) introgressed from G. barbadense L. originally identified in 'Sealand 883'. The QTL was deployed within four genetic backgrounds: Acala SJ4, Paymaster HS26, Deltapine 50 (DP 50), and Georgia 2004089 (GA089), each representing the gene pools of the major US cotton‐growing regions: the US Southwest, Texas High Plains, Mississippi Delta, and US Southeast, respectively. In highly related bulked sister lines (BSLs), the effect of qFL‐Chr.25 was significant in the DP 50 (1.4 mm) and GA089 (1 mm) backgrounds in trials grown in Tifton, GA, in 2014 and 2015. In multilocation trials planted across the Cotton Belt in 2011 of 25 lines from each of the four backgrounds carrying the G. barbadense allele and 25 without the introgressed allele, FL of the QTL(+) lines were numerically higher than the QTL(−) lines by 0.9 mm, though not statistically significant. Recombinant genotypes recovered from the Paymaster HS26 and GA089 backgrounds, and development of additional simple sequence repeat (SSR) markers within the QTL region, allowed further refinement of the qFL‐Chr.25 region's boundaries from ∼2.2 to 0.8 Mb. Although variable effects were seen from this QTL, observation in a more isogenic state such as the BSLs and recombinant lines made the effect of the QTL more apparent. Incorporation of this QTL into breeding programs aided by these newly developed SSR markers should help in the utilization of this introgression to improve cotton fiber quality. [ABSTRACT FROM AUTHOR]

Previous studies revealed difficulties in retention and recombination of alien species germplasm by conventional introgression in upland cotton (Gossypium hirsutum L.) due to incompatibility at the whole-genome level. An alternative approach is to use alien species chromosome substitution (CS) lines, whereby retention and recombination can be differentially increased for a specific chromosome or chromosome segment. Here we report for the first time on the development of a set of CS lines from two alien species in a common genetic background of upland cotton. The overall objective of this research is to report on the chromosomal association of important fiber traits using a partial-diallel mating design among CS lines of G. tomentosum Nutt. Ex Seem (CS-T), a wild tetraploid species endemic to Hawaii, G. barbadense L. (CS-B), a cultivated tetraploid species with improved fiber quality traits, and 'TM-1' (G. hirsutum), the recurrent parent with improved agronomic traits and moderate fiber quality traits. The genetic effects associated with CS lines were dissected into additive, homozygous dominance, and heterozygous dominance genetic effects using an additive-dominance statistical model. Five of six CS-B lines and two of six CS-T lines had significant additive genetic effects on lint percentage, indicating that the respective substituted alien chromosome carried alien alleles with potential to improve lint percentage in upland cotton. Fifty-six percent of 16 different significant additive effects associated with the CS-B lines could be useful to improve fiber traits in TM-1. On the contrary, 40% of 15 significant additive genetic effects of the CS-T lines had potential to improve fiber traits. Results suggested that CS lines can unveil many beneficial alleles harbored cryptically in the other AD-genome species and render them more accessible for research and cotton genetic improvement. [ABSTRACT FROM AUTHOR]

Chromosome substitution lines (CSLs) have been developed for selected chromosomes from two tetraploid species of Gossypium and are effective ways to target introgression of alleles from exotic tetraploid species into Upland cotton (G. hirsutum L.) Genetic effects of chromosomes 1, 4, and 18 from Upland cot- ton (TM-1), Pima cotton (G. barbadense L.), and Hawaiian cotton (G. tomentosum Nutt. ex Seem) were estimated by topcrossing TM-1 and six isochromosomal CSLs with fve upland cultivars and comparing F2 and F3 hybrids for agronomic and fiber traits. Data were analyzed according to an additive-dominance (AD) model. Additive genetic effects were greater than dominance effects for lint percentage, fiber uniformity, fiber strength, and elongation; whereas, dominance effects were greater than additive effects for boll weight, lint yield, fiber length, and fiber micronaire. All additive x environment effects were small. Dominance x environment effects were only significant for boll weight, lint yield, and fiber micronaire. Chromosome B04 and B18 from Pima cotton and T01 from Hawaiian cotton had significantly greater additive effects for lint percentage than homologs. Chromosomes 1, 4, and 18 from the three species generally showed negative additive effect on lint yield compared with cultivars. Chromosome 1 from Hawaiian cotton had greater additive effects on fiber length than homologs. Chromosomes 1 and 4 from Pima cotton showed greater additive effects on fiber strength than homologs. The magnitude of additive effects on important agronomic and fiber traits show that Pima cotton and Hawaiian cotton harbor useful alleles for Upland cotton breeding programs. [ABSTRACT FROM AUTHOR]