Ibrokhim Y. Abdurakhmonov

Toward Sequencing Cotton (Gossypium) Genomes

Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton ( Gossypium spp.)

Application of Association Mapping to Understanding the Genetic Diversity of Plant Germplasm Resources

Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a “powerful gene tagging” tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application.

Small RNA regulation of ovule development in the cotton plant, G. hirsutum L

BackgroundThe involvement of small RNAs in cotton fiber development is under explored. The objective of this work was to directly clone, annotate, and analyze small RNAs of developing ovules to reveal the candidate small interfering RNA/microRNAs involved in cotton ovule and fiber development.ResultsWe cloned small RNA sequences from 0–10 days post anthesis (DPA) developing cotton ovules. A total of 6691 individual colonies were sequenced from 11 ovule small RNA libraries that yielded 2482 candidate small RNAs with a total of 583 unique sequence signatures. The majority (362, 62.1%) of these 583 sequences were 24 nt long with an additional 145 sequences (24.9%) in the 21 nt to 23 nt size range. Among all small RNA sequence signatures only three mirBase-confirmed plant microRNAs (miR172, miR390 and ath-miR853-like) were identified and only two miRNA-containing clones were recovered beyond 4 DPA. Further, among all of the small RNA sequences obtained from the small RNA pools in developing ovules, only 15 groups of sequences were observed in more than one DPA period. Of these, only five were present in more than two DPA periods. Two of these were miR-172 and miR-390 and a third was identified as 5.8S rRNA sequence. Thus, the vast majority of sequence signatures were expressed in only one DPA period and this included nearly all of the 24 nt sequences. Finally, we observed a distinct DPA-specific expression pattern among our clones based upon sequence abundance. Sequences occurring only once were far more likely to be seen in the 0 to 2 DPA periods while those occurring five or more times were the majority in later periods.ConclusionThis initial survey of small RNA sequences present in developing ovules in cotton indicates that fiber development is under complex small RNA regulation. Taken together, the results of this initial small RNA screen of developing cotton ovules is most consistent with a model, proposed by Baulcombe, that there are networks of small RNAs that are induced in a cascade fashion by the action of miRNAs and that the nature of these cascades can change from tissue to tissue and developmental stage to developmental stage.

Phytochrome RNAi enhances major fibre quality and agronomic traits of the cotton Gossypium hirsutum L

Simultaneous improvement of fibre quality, early-flowering, early-maturity and productivity in Upland cotton (G. hirsutum) is a challenging task for conventional breeding. The influence of red/far-red light ratio on the fibre length prompted us to examine the phenotypic effects of RNA interference (RNAi) of the cotton PHYA1 gene. Here we show a suppression of up to ~70% for the PHYA1 transcript, and compensatory overexpression of up to ~20-fold in the remaining phytochromes in somatically regenerated PHYA1 RNAi cotton plants. Two independent transformants of three generations exhibited vigorous root and vegetative growth, early-flowering, significantly improved upper half mean fibre length and an improvement in other major fibre characteristics. Small decreases in lint traits were observed but seed cotton yield was increased an average 10-17% compared with controls. RNAi-associated phenotypes were heritable and transferable via sexual hybridization. These results should aid in the development of early-maturing and productive Upland cultivars with superior fibre quality.

Genomics-Assisted Plant Breeding in the 21st Century: Technological Advances and Progress

One of the key global challenges of the 21st century is the production of enough food for the increasing world population. As per some recent reports the global population will continue to grow with some 9 billion people by the middle of the current century and the world will need 70 to 100% more food by that time (Godfray et al., 2010 and references therein). Agricultural productivity needs to be increased while addressing the issues of scarcity of arable land and water, impact of changing climate and preservation of natural resources. Improvement of crop yields on available agricultural land requires concerted efforts using modern scientific and technological advances in multiple disciplines (Hubert et al., 2010). Two such disciplines that have revolutionized crop improvement in the recent decades are molecular breeding and plant genomics. While the availability and application of molecular markers have accelerated the pace and precision of plant genetics and breeding, the introduction of a multitude of “omics” tools has provided unprecedented ability to dissect the molecular and genetic basis of traits as well as the characterization of whole genomes.

RNA Interference for Functional Genomics and Improvement of Cotton (Gossypium sp.)

RNA interference (RNAi), is a powerful new technology in the discovery of genetic sequence functions, and has become a valuable tool for functional genomics of cotton (Gossypium sp.). The rapid adoption of RNAi has replaced previous antisense technology. RNAi has aided in the discovery of function and biological roles of many key cotton genes involved in fiber development, fertility and somatic embryogenesis, resistance to important biotic and abiotic stresses, and oil and seed quality improvements as well as the key agronomic traits including yield and maturity. Here, we have comparatively reviewed seminal research efforts in previously used antisense approaches and currently applied breakthrough RNAi studies in cotton, analyzing developed RNAi methodologies, achievements, limitations, and future needs in functional characterizations of cotton genes. We also highlighted needed efforts in the development of RNAi-based cotton cultivars, and their safety and risk assessment, small and large-scale field trials, and commercialization.

Chromosome Substitution Lines: Concept, Development and Utilization in the Genetic Improvement of Upland Cotton

Cotton is the most important natural fiber source for the textile industry world-wide. It is also an alternative of the man-made petroleum-based “synthetic fibers” providing an advantage for a sustainable environment. Cotton is formed by developing seed of several Gossypium species, which are mainly grown as an important cash crop in more than 70 countries including USA, India, China and Uzbekistan (Smith and Coyle, 1997). Although cotton plants are best known as the renewable source of textile materials for clothing, the fiber, seed and plants have many other uses, including home insulation to save energy, protein-rich seedderived feed for animals, cottonseed oil as a foodstuff for humans, and as a source of mulch and biomass (Cotton Incorporated, 2010, http://cottontoday.cottoninc.com/sustainabilityabout/responsible-economic-development, verified on October 14, 2011). This brings significant humanitarian and economic benefits. For example, scientists are exploring genetic means to better harness its highly nutritious seed for food and feed (Sunilkumar et al., 2006).

Genetic Diversity in Gossypium genus

Cotton (Gossypium spp.) is the unique, most important natural fiber crop in the world that brings significant economic income, with an annual average ranging from

Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in Upland cotton (Gossypium hirsutum L.).

27 – 29 billion worldwide from lint fiber production (Campbell et al., 2010). The worldwide economic impact of the cotton industry is estimated at ~

Methodologies for In Vitro Cloning of Small RNAs and Application for Plant Genome(s)

500 billion/yr with an annual utilization of ~115-million bales or ~27-million metric tons (MT) of cotton fiber (Chen et al., 2007). In 2011 and 2012, global cotton production is projected to increase 8% (to 26.9 million MT). This will be the largest crop since 2004 and 2005 (International Cotton Advisory Committee [ICAC], 2011).