Germplasm and Genetic Stocks

Improvement of drought tolerance is one of the greatest needs of the cotton industry, but also one of the most challenging of all breeding objectives. Studies at Texas A&M University have focused on inter-relating measurable drought related traits within the context of genotype differences. Traits of interest included seedling drought mortality, root architecture and biomass, leaf temperature, normalized difference vegetative index, stomatal conductance, chlorophyll concentration, image analysis, lint yield, and fiber qualities. The strategy to our approach was to determine drought-related traits that could be efficiently measured and converted to high-throughput phenotyping systems in field conditions. Such a system would enable field phenotyping on a scale that could accompany the rapid advances in genotyping technologies therefore creating and applying a field-based phenomics approach to cotton breeding programs.

As the global population increases, providing food, fiber and fuel to meet growing demand has become a significant challenge. Texas A&M University is training future plant breeders to meet this challenge and recently expanded their effort through a Distance Education Program in Plant Breeding. The Soil and Crop Sciences Department at Texas A&M University offers a wide range of distance education opportunities. The plant breeding distance education program offers online Masters and Ph.D. degrees in Plant Breeding as well as a robust continuing education program for agriculture professionals seeking further plant breeding education but who are not interested in a degree program. The Texas A&M Plant Breeding and Genetics Continuing Education Program is designed to convey knowledge about crop genetics and improvement to industry technical and professional personnel who wish to refresh their knowledge in specific areas of plant breeding and genetics, participants who want to gain a professional certificate in plant breeding and genetics, and others who simply want to know more about plant breeding and genetics.

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 damage, abscission, and subsequent yield-loss. Previous studies in Upland cotton (Gossypium hirsutum) indicate that plant trichome density plays an important role in conferring resistance to cotton fleahopper, but the mechanism of resistance remains largely unknown. In this project, an RNA sequencing experiment was performed to measure gene expression in four Upland cotton genotypes on which the cotton fleahopper had fed and on which the insect had not fed. Genotypes were selected for testing based on previous data regarding their level of susceptibility or resistance to cotton fleahopper feeding damage. RNA sequencing was performed using the Illumina HiSeq 2000 platform, and Gossypium raimondii was used as the reference genome.

An understanding of the genetic diversity of cotton (Gossypium spp.) is essential to develop strategies for collection, conservation, and utilization of these germplasm resources. To define the diversity present in the U.S. National Cotton Germplasm Collection, a core set of 105 SSR markers were applied to analyze molecular relationships among 2,254 selected accessions, collectively known as the Gossypium Diversity Reference Set (GDRS). NTSYS software was used to generate a Jaccard similarity matrix of the accessions which was double-centered and used to calculate eigenvectors for plotting Principal Coordinate Analyses (PCoA). The first two principal coordinate axes explained ~27% of molecular variation among accessions. Two distinct clusters could be discerned among AD genome accessions that corresponded to the G. hirsutum and G. barbadense species. A third distinct cluster composed of A genome accessions was evident, and accessions of the remaining diploid genomes formed a fourth intermixed but distinct cluster. Accessions could be identified within the G. hirsutum and G. barbadense clusters that were either misclassified or the product of introgression. Structure could be discerned within G. hirsutum that related to recognized races, but distinct race clusters were not evident. Cultivated accessions of G. hirsutum were primarily confined to a small portion of the G. hirsutum cluster that also corresponded with the race latifolium - indicating the large contribution of that race to the variability observed in cultivated cotton. A good resolution of the diversity present in the cultivated tetraploid species was achieved, and will aid in maintaining the diversity and integrity of these species in the collection. However, weak resolution of variation among diploid species indicates a need for more informative markers to be developed to better define the diversity of those species within the germplasm collection.

Endemic cotton(Gossypium herbaceum) cultivars possess characteristics of course fiber (micronare >5) and short staple (18-22mm) while upland cotton cultivars produce fibers with micronare lesser than 5 and 28-32 mm length. In this study 10 endemic cotton cultivars were used at Varamin and Kashmar stations for crossing with arboreum species, cultivar VTDL which have good fiber quality and has been introduced from India. In 2nd an 3rd years all F1 hybrids were crossed with their herbaceum parent. The Hybrids showed high value of fiber quality. F1 Bandar-Abass x arboreum was with highest span length fibers (27.6mm). In the third year back-cross of the mentioned hybrid along with two other back-crossed of Sabzevar x VTDL and Sahreza x VTDL showed highest span length fibers ( 23.5, 24.6 and 25.1 mm acordingly ). While maximum value of span length fiber in herbaceum cultivars was 22.6mm. In fourth year all back-crosses along with F3 and parents seeds were grown and selection as well as back-crossing was carried out. Totally, results showed that fiber length of cultivars like Qum could improve through crossing with arboreum. Since there is high level of variability among each group of offspring resulted from crosses, hence selection for fixing the traits and discovering of elite plants in view of various characteristics is essential.

In this project in order to increase salt-tolerant of commercial cultivars, those lines were used that selected from saline lands of sadoddin cotton farms in Kashmar. These lines possessed high growth ability under saline stress with small boll growth size. In order to improve salt-tolerant lines with upstanding vegetative growth under salt stress conditions, crossing were done between commercial cultivars namely, Varamin, Sahel, Bakhtegan and Mehr and selected lines. This followed by several back crossing at Varamin station and screening of offspring under saline condition at Sadoddin station at the next of each year. This operation repeated during 4 years and in the last year several elite plants were selected from both stress (kashmar) and non-stress (varamin) of salinity. The results reveal that average value of measured traits of selected lines were superier than their commercial parents under both conditions of stress and non-stress of salinity. For example, average seed cotton plant yield of improved lines which derived from Mehr cultivar crosses was 109.9 gr, while under salt stress conditions the same in Mehr cultivar was 55.3 gr. Also under non-salt stress condition, average seed cotton of these lines was 145.9 gr but in their maternal parent (cv. Mehr) it was 108 gr. The main conclusions describe that resulted populations from crosses posses some economically significant traits, especially under salt stress conditions which made them superior than their parents and such a large generated diversity could be used for elite genotypes in further breeding researches.

In order to evaluation of yield potential, early maturity and other quantitative and qualitative properties of cotton mutant lines for breeding programs, a field experiment was carried out in eight research stations during 2008-2009. The six mutant lines (L-M-1425, LM- 1676, L-M-1321, L-M-1673, L-M-1303, and L-M-1373) and 4 commercial varieties were arranged in completely randomized block with four replications. Different traits as yield, yield components, earliness and qualitative characteristics were studied. The results showed a significant difference among all traits. L-M-1673 line was more earliness than other lines. LM- 1676 and L-M-1425 in mazandaran, L-M-1676 in Moghan stations, L-M-1321 line in Darab and Varamin station, L-M-1321 and L-M-1425 in Kashmar station , L-M-1303 and LM- 1676 in HashemAbad and L-M-1425 in Karkandeh Station have the highest seed cotton yield. The results of combined Analysis showed that L-M-1321, L-M-1676, L-M-1425 were superior than others lines, respectively.

Leaf Curl Virus disease is one of the major impediments constituting a primary limit on the productivity of cotton particularly in Punjab province. This menace has brought about a huge loss of about Rs. 9 billion to the economy of Pakistan during the last fifteen years. Since the resurgence of new strain of cotton Leaf Curl Virus (Burewala Cotton Leaf Curl Virus) in 2001, ten thousands lines (local as well as exotic) of Gossypium (upland cotton) have been screened during the last five years (2003-2007) at Cotton Research Station, Vehari (Cotton Research Institute, Ayub Agri. Institute, Faisalabad) but no resistant material have been identified. Gossypium arboreum (desi cotton) occupying 5% of the total area under cotton in Pakistan has been found resistant to Cotton leaf Curl Virus disease since the appearance of this disease in Multan (Pakistan) during 1967. Therefore introgression of CLCV resistance genes from Gossypium arboreum and other wild species into cultivated upland cotton (Gossypium hirsutum) is of vital importance in solving this hazardous problem. Moreover Gossypium tomentosum will also be used to transfer CLCV resistance into upland cotton. However main focus will be on G. arboreum.

Advances in genetic engineering in recent years have led to the development of plants that are resistant to some insects through incorporation and expression of genes encoding delta-endotoxins (δ- endotoxins) from the bacterium Bacillus thuringiensis. As transgenic crops have revolutioned the world agriculture on one side, there has been a great concern regarding the impact of these transgenic food on animals and human being which are the main consumers of transgenic feed. A 120 days study was carried out to evaluate the potential risk of transgenic Bt diet on experimental rats. Weight gained/loss, mortality/survival, insecticidal gene integration and expression, biochemical and histological studies were the main parameters undertaken to investigate effect of transgenic Bt diet in these animals. No lethal effects of transgenic Bt diet on both groups of animals were observed. Rats had very similar growth pattern when fed either Bt transgenic or non Bt diet. No significant differences in relative weights observed during the entire period of study. No any evidence of insecticidal gene integration and expression was found. Histological and biochemical tests also suggested that transgenic diet did not make any significant morphological and physiological differences among experimental organisms.

The cytoplasmic male sterility (CMS) system is convenient and efficient for cotton hybrid seed production. However, because of the limited restorer lines carrying the restorer gene Rf1, it has not been widely used. So, to improve the efficiency of restore line breeding, we want to develop some new tightly markers related to Rf1 gene. In this study, the fertility segregation in a backcross (BC8F1) population of 409 individuals and an F2 population of 695 plants confirmed that the fertility restoration of CMS-D2 was determined by one dominant restorer gene (Rf1). Subsequently, 13 Rf1-linked simple sequence repeat (SSR) markers were identified from 8248 pairs of SSR primers. A combined map showed that the 13 polymorphic SSR markers were mapped in a region of 0.279 cM encompassing the Rf1 gene. Sequence alignment showed that they were distributed on nine scaffolds of chromosome 9 in the sequenced D5 genome of G. raimondii. Then, ten pentotricopeptide repeat (PPR)-like genes were identified on two of the nine scaffolds, including Scaffold 333 where nine PPR-like genes were clustered in a region of about 160 kb with marker BNL3535 in. Among them, PPR-like gene Cotton_D_gene_10013437 was the nearest gene with BNL3535, comparative sequence analysis of the homologous gene among sterile (A), maintainer (B) and restorer (R) lines, and co-segregation analysis further confirmed that this gene maybe the candidate for the Rf1 gene. Compared with the non-restoring lines, the restorer had a 9-nucleotide (nt) insertion and a single nucleotide polymorphism (SNP) 8 nt upstream of the insertion at the 3' untranslated regions (3' UTRs) in this gene. And this SNP leads to the deficiency of a cleavage site for restriction enzyme DraI in the restorer line, so then a cleaved amplified polymorphic sequence (CAPS) marker named CAPS-R was developed from the SNP site, and was further used to track the restorer gene and its homozygous or heterozygous status in molecular breeding for restorer lines. In our previous study, a CMS-D2 cytoplasm-specific SCAR marker has beed developed, and can be used to identify the CMS-D2 cytoplasm. So, here a marker-assisted selection system using the Rf1-specific CAPS-R marker and a CMS-D2 cytoplasm-specific SCAR marker was established to distinguish the three-line hybrids from other genotypes and artificial emasculation and pollination.