Germplasm and Genetic Stocks

Genetic diversity is desirable for long term crop improvement and reduction of vulnerability to important crop stresses. Many successful cotton cultivars have been developed from closely related parents but limited yield gains in recent years have led some to advocate more extensive use of exotic germplasm (Meredith 1991).Gossypium arboreum possesses many favourable traits for cotton production which the tetraploid cultivars lack. For example drought tolerance, resistance to disease, make G. arboreum well adapted to dry land conditions and low input cultivation practices. Some of the accessions produce fibres with high strength and seeds with high oil content and seed index. The G. arboreum germplasm collection is an invaluable genetic resource for tetraploid improvement; however it has not been well characterised at the molecular level.Microsatellite markers showed considerable genetic variation among the seventeen genotypes of cotton Gossypium arboreum species.The similarity coefficient ranged between 0.78 to 1.00.The maximum numbers of polymorphic bands were obtained from marker MGHES-13 and JESPR-65. Understanding the genetic relationships within G. arboreum would facilitate efficient use of resource for developing superior cotton cultivars with favourable agronomic traits.

In this study, we analyzed the chromosomal deficiency of 14 monosomic lines in the Uzbek Cotton Cytogenetic collection. Hybrids were created between the monosomic individuals of the Uzbek Collection and chromosomally identified homozygous reciprocal translocation lines of the Cotton Cytogenetic Collection at Texas A&M University. The monosomes were identified by analyzing meiotic metaphase I configurations of the synthesized monosomic translocation heterozygous F1 hybrids. When the monosome of such a hybrid involves neither of the translocated chromosomes, each metaphase-I cell typically includes a quadrivalent and a monosome (23 II + IV + I); when the monosome involves one of the translocated chromosomes, a trivalent typically occurs (24 II + III). For example, we observed had 24 bivalents + 1 trivalent in metaphase-I cells of the 2n-1 F1 hybrids resulting from crosses of Mo4 with the translocation line TT 13R-19R, which shows that Mo4 is either the chromosome 13 or 19. Similarly, 2n-1 F1 hybrids from cross Mo62 with translocation line TT 14R-24R formed 24 bivalents + 1 trivalent, which shows that Mo62 is either chromosome 14 or 24; we observed that Mo62 has a “reduced” stigma, which can serve as a new phenotypic marker. Two other monosomics, Mo73 and Mo90, have been associated with the tester lines TT 9R-17Ra and TT 5R-23R, respectively. However, tests of several other monosomics in the Uzbek Collection, such as Mo69, Mo71, Mo58, Mo72, Mo84, Mo85, have not shown any common chromosome pairing with tester translocation lines of known chromosomes, suggesting that additional tests are needed to identify these monosomics. The details of the translocation tests conducted will be presented.

To understand the genetic basis of the elite cotton germplasm in China, a total of 83 SSR markers (an average of three on each of the 26 chromosomes ) were randomly selected to analyze population structure and genetic diversity of 158 elite G. hirsutum variety accessions from the China cotton germplasm collection, which were collected from different cotton growing areas in China (114) as well as from American (39), Africa (3), Former Soviet Union (4), and Australia (1). 247 allelic variations were detected with an average allele number of 2.89. The average PIC ( polymorphism information content) and gene diversity values were determined to be 0.3534 and 0.4261, respectively, indicating a relatively low degree of genetic diversity. Phylogenetic analyses revealed genetic distance (GD) of all elite G. hirsutum variety accessions ranged from 0.0244 to 0.6743 with an average of 0.4234. The average GD within the G. hirsutum variety accessions of specific ecotypes (China, America, Former Soviet Union, and Africa) was very close and ranged from 0.4164 to 0.4348. The highest GD (0.673) among all elite G. hirsutum variety accessions was observed between the variety Handan33 (from China) and AcalaB (from America). The highest GD (0.6535) within the G. hirsutum variety accessions of specific ecotypes was observed between the variety Zhongmiansuo12 (an improved cultivar) and ZhongARC185（an innovative line）, both form the Chinese ecotype group. American varieties had the highest average GD (0.4348) and Chinese varieties had the lowest. By population structure ( Bayesian clustering) analyses, the 158 genotypes were assigned into two subgroups (i.e. SG1 and SG2) with a wide range of gene flows among the cotton germplasm from China and from America. The two subgroups inferred from structure did not show an association with the geographic origin of the materials, reflecting the probable extensive exchange of parental lines by breeders nationwide. Using a probability of membership threshold of 60%, 61 lines were assigned to SG1, 60 lines to SG2 and the remaining 37 lines were considered as intermediates. Furthermore, we performed an independent STRUCTURE run for each of the two subgroups. The results indicated there were two and five sub-subgroups existed in the subgroup SG1 and SG2, respectively, which accorded with the seven subgroup when running the structure using all 158 accessions in one. These results have provided valuable information for the association mapping of important agronomic traits, as well as for the breeding and exploit of new cotton germplsm.

Cotton fibre is an unique in nature as it is a single cell known so far as longest in length. The fibres are the out growths of few cells (15-20%) from the surface of the epidermal layer of cotton seed (ovule). There are two classes of seeds in cotton viz., fuzzy seeded cotton with fibres and fuzziless with fibres. In one class, called fuzz, epidermal cells just initiate to elongate but do not go beyond 5 mm (Stewart 1975). They represent about 80% in fuzzy type of seed. Remaining cells of about 20% are known to elongate beyond 5mm and go upto 40mm.Varities of G.hirsutum, G.herbaceum and G.arboreum fall in this class. In fuzzy less type of seeds,there are no short fibres,initiated cells (15-20%) elongate beyond 5mm -45mm.Genotypes of G.barbadense fall in this class. Proportion of cells elongating from epidermal cells of a cotton ovule determines the economic value of cotton in terms of lint yield expressed as ginning out turn. Higher the ginning out turn, higher the lint yield (cotton excluding seeds). In the present study, we found the presence of genetic variability for number cells to elongate into fibre from the cross between normally linting cotton genotype (38% GOT) and lintless cotton (0.01% GOT). Based on F2 data during 2010-11 at Agricultural Research Station Dharwad (INDIA), it is concluded that fibre cell elongation is the result of interaction between two independent genes (dominant duplicate gene interaction, 15 fibred :1 fibreless) classifying plants in two phenotypic groups viz., fibred (irrespective of number of cells elongated) and fibreless. As many as 147 F3 progenies were evaluated at the same location during 2011-12. All plants of eight progenies derived from eight F2 plants which were fibreless were also fiberless in F3. All plants of 108 progenies were fibred. In fully fibred plants, counting number of cells was not possible and considered as many fibres per 9.0 sq.mm. Segregation for number of cells elongating was observed in 31 progenies. As many as 91 plant’s seeds were observed for number of cells elongated and were grouped into 5 phenotypic classes. The another group was the fully fibred plants. Number of cells elongating into fibre (more than 10 mm long) per 9 sq. mm on matured seed surface was recorded under steareomicroscope ( Labomade Make) at 50x magnification.The range of number of elongating cells varies from 20-30, 31-40,41-50,51-60, 61-70,71-80 per 9.00 sq.mm. The ginning out turn (proportion of lint in seed cotton which is positively correlated to number of elongating cells per unit area) is also recorded. Ginning out turn was in the range between 0.01 -42 percent across the group. Length of the fibre also determines the ginning out turn. Presence of genetic variability for GOT visa visa number cells per unit area and length of those elongated cells was recorded. These lines will be of immense use to identify diverse genes involved in determining the number cells to be elongated through transcriptome/proteome studies. Diversity due to SNPs can also be detected for the genes.

Virescent leaves are an important character of plant that can be inherited in cotton (Gossypium hirsutum L.). Most of which suggested that this trait was controlled by one recessive gene in nucleus. It was well known that this genetic mutation could be generated by nature condition, physical treatment (for example, γ-irradiation) and chemical treatment (for example methylnitrosourea and ethyl methanesulfonate) and tissue culture. Here we reported identification of a virescent mutation (vsp) after exposing the upland cotton (Gossypium hirsutum L.) CCRI58 seeds in space environments. vsp mutant was characterized at the morphological, agronomic, cellular and genetic levels. vsp mutant showed an earlier virescence and specific only to true leaves. Agronomic traits of vsp mutant, such as plant height, number of bolls, boll weight, yield and fiber quality were significantly lower than those of CCRI 58. Chlorophyll level, carotenoid level and photochemical efficiency of vsp mutant true leaves were significantly lower compared to CCRI 58 at young leave stage. Anatomical studies of chloroplasts showed that vsp mutant lacked grana in the thylakoids of the mesophyll cells at young leave stage, while CCRI 58 showed normal grana in the thylakoids of the mesophyll cells at young leave stage. This indicated that chlorophyll and carotenoid levels were related with chloroplast structure. In order to clone the candidate genes of the virescence trait, F2 segregation population was built by crossing parents between vsp as materal and TM-1 as paternal. The principium gene mapping of Virescent mutation was made by getting polymorphic markers. The fine gene mapping of virescent mutation was made by getting polymorphic markers from F2 large segregation population. The differentially expressed genes are identified by bioinformatics analysis of RNA transcriptome sequencing data. It would be explained the molecular mechanism of the virescent mutation and application of virescent mutant in cotton breeding programs. Key words: the short season cotton, virescent mutation (vsp), molecular mechanism, the principium gene mapping, the fine gene mapping, the differentially expressed genes.

Cotton fleahopper (Pseudatomoscelis seriatus) (Hemiptera: Miridae) is a piercing-sucking insect that has emerged as a major pest in the Texas cotton industry over the past decade. Cotton fleahopper feeding results in square abscission and damage and subsequently, yield loss. Current control measures for cotton fleahopper are predominated by chemical pesticides. Variation in resistance to the cotton fleahopper has previously been noted in cotton cultivars (G. hirsutum), but the mechanism of resistance remains largely unknown. This project focuses on breeding towards increased resistance to cotton fleahoppers in two susceptible, high yielding lines by backcrossing with genotypes previously identified as potentially resistant. Screening efforts, thus far, indicate that plant trichome density plays an important role in conferring resistance, as measured by square retention under cotton fleahopper pressure. Efforts are currently underway examine variations in pubescence and trichome morphology that may influence cotton fleahopper feeding.

The primary value of a cotton crop is fiber, but seed is an important by-product. Cottonseed use is limited by the presence of gossypol, which is a toxic compound to non-ruminant animals including humans. Glandless cotton plants that do not contain gossypol are highly susceptible to pests. Recently, researchers at Texas A&M University developed cotton plants with normal gossypol glands in vegetative tissue and ultra-low gossypol (ULG) levels in the seed, making these suitable for human consumption. The objective of this study was to integrate this trait into elite germplasm, develop techniques to enhance this breeding procedure, and measure performance of newly converted germplasm. The backcross method was used to introduce the ULG trait from transgenic ‘Coker 312’ plants into four elite lines from the U.S. and two lines developed in East Africa. Phloroglucinol and NIR spectroscopy assays were tested to screen for ultra-low gossypol both in the seed and in seedlings in order to make the selection process efficient. The phlorogucinol assay was a better predictor of the ULG trait in comparison to NIR. Converted lines were tested in field trials at College Station, TX, in 2011 and 2012. Preliminary results suggest the integration of ULG does not affect the production potential of the various genotype backgrounds. A successful introgression program will result in cotton cultivars that provide substantial sources of high-value fiber and feed products.

The exotic gene pools of the tetraploid Gossypium species G. barbadense, G. tomentosum, and G. mustelinum (2n=52), the sanctuaries of many useful genes and genetic variability, have been under characterized and underutilized in the genetic improvement of Upland cotton (G. hirsutum). Cytological evidence and comparative molecular mapping results suggested that structural genomic differences among the tetraploid cotton species are minimal and do not preclude introgression of the alien species gene pools into Upland cotton. Nonetheless, previous interspecific introgression efforts with Upland cotton using conventional breeding methods had limited success, which suggests that many interspecific recombinants do not occur, are "lost", or are selected against under conventional breeding practices. Scientists at Texas A&M University and USDA/ARS, Mississippi State have been collaboratively developing sets of backcrossed chromosome substitution lines (CS) for different chromosomes and chromosome segments of G. barbadense, G. tomentosum and G. mustelinum. Backcrossed five generations to a common inbred, these CS lines are largely isogenic, except for the differences between the substituted pair of chromosomes or chromosome segments in each CS line. Once developed, CS lines can be used in diverse manners for breeding, quantitative genetics and genomics of complex multigenic traits, including agronomic and fiber quality traits. The overall objective of this paper is to report on the field evaluation of agronomic and fiber quality traits of the CS lines. We have used several types of population structure, experimental design and statistical analysis to discover the alien chromosomal effects on important complex traits using the CS lines. The near-isogenic nature of the substitution lines to the common parent TM-1 provides a unique opportunity to use specific mating designs among the CS lines of interest to create different chromosome specific combinations of unique genetic resources. Our results show that the CS lines are useful from several perspectives: 1) to improve genetic diversity for important traits in Upland cotton, 2) to discover the untapped potential of cryptic alleles from the wild and unadapted tetraploid species, 3) to understand the ramifications of epistasis on complex agronomic and fiber traits and 4) to identify chromosomal locations of important fiber and agronomic traits. CS lines can lead to enhanced resolution in linkage mapping and facilitate targeted exploitation of exotic germplasm to improve fiber quality and agronomic traits in cotton breeding program. CS lines thus provide a powerful resource for innovative utilization of genetic resources and a tool to overcome the problem in interspecific introgression in genetic improvement of Upland cotton.

Cultivated upland cotton germplasm was derived from a small number of ancestral cottons and therefore has narrow genetic base. Establishing the genetic diversity is essential for the germplasm enhancement, and genomic analysis in cotton. With a goal to sample the upland cotton genetic diversity and to utilize it in mapping and genomic selection in cotton improvement programs we genotyped the upland cotton germplasm. We characterized genetic relationships of 384 upland cotton cultivars, representing breeding programs from across the U.S. cotton belt. Genotyping was done using high-resolution capillary-based SSR genotyping. SSR marker sequences were obtained from Cotton Marker Database and a minimum of four markers per chromosome were selected. The structure of genetic diversity of upland cultivars in the form of phylogenetic tree and the genetic relationships of the cotton cultivars using marker data will be presented.

In the past century, cotton has been adapted to the low desert, irrigated production areas of central Arizona. Despite progress, it will be perhaps a greater challenge to further increase the yield of cotton in this period of global climate change and diminishing fresh water supplies. Genetic improvement of cotton via modern plant breeding is the most sustainable and economical approach to address these eminent problems. However, the development of superior heat tolerant and water-use efficient cotton cultivars has been slowed by the polygenic inheritance and relatively lower heritability of economical traits in stress environments. Moreover, there is limited knowledge of the key genes that underpin physiological and biochemical traits that relate to improved productivity under high temperatures and water deficit. To that end, we developed genotyping-by-sequencing (GBS) and field-based, high-throughput phenotyping (HTP) approaches for dissecting the genetic architecture of adaptive traits that are potentially important for increased cotton fiber yield and quality in the southwestern United States. We tested these approaches on a cotton recombinant inbred line (RIL) population (TM-1×NM24016) grown under replicated well-watered and water-deficit treatments in Arizona. We present results from a statistical genetic analysis of phenotypic data that were predominantly collected with tractor-mounted sensors and suggest how powerful modern plant breeding tools can be leveraged in the genetic improvement of cotton.