Wild species of Gossypium present an impressive range of variation in many characters, all of which can potentially be exploited in cotton improvement programs. G. anomalum possesses several desirable characters such as extremely fine fibers, immunity to black arm and bacterial blight disease and tolerance to water deficit, as this species is endemic to relatively dry areas. To effectively introgression desirable traits into cultivated cotton from G. anomalum, we made crosses between G. hirsutum (A1A1D1D1) and G. anomalum (B1B1) and obtained triploid hybrids with the genome composition A1D1Bl. Then we treated triploid hybrids with 0.15% colchicine and obtained a putative fertile hexaploid (A1A1D1D1B1B1) in order to resolve interspecific hybrid sterility problems. We demonstrated the hybridity and doubled status of a (G. anomalum × G. hirsutum)2 hexaploid using morphological, cytological and molecular marker methods. To effectively monitor G. anomalum genome components in the G. hirsutum background, we developed 5974 non-redundant G. anomalum derived SSR primer pairs using RNA-Seq technology, which were combined with a publicly available physical map. Based on this combined map and segregation data from the BC2F1 population, we identified a set of 230 informative G. anomalum-specific SSR markers distributed on the chromosomes, which cover 95.72 % of the cotton genome. After analyzing BC2F1 segregation data, 50 recombination types from 357 recombination events were identified, which cover 81.48 % of the corresponding G. anomalum genome. A total of 203 recombination events occurred on chromosome 11, accounting for 56.86 % of the recombination events on all chromosomes. By successive backcrosses and selfing combined with marker assisted selection, about 60 chromosome segment substitution lines (CSSLs) were developed. Genomic regions that affect fiber quality, plant height and boll size were identified. This study represents an important step towards introgressing desirable traits into cultivated cotton from the wild cotton species G. anomalum.

Laccase gene, GhLAC15, enhanced Verticillium wilt resistance via increasing defense-induced lignification and arabinose and xylose accumulation in the cell wall of Gossypium hirsutum YanZhang#, Li-zhuWu#, Xing-fenWang, Zhi-kun Li, Jun Yang, Guo-ningWang, Yuan-yuanYan, Jin-huaWu, Li-qiangWu, Gui-yinZhang, Zhi-yingMa* College of Agronomy, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Co-Innovation Center For Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding 071001, China. #These authors contributed equally to this work. *Correspondence: mzhy@hebau.edu.cn Tel: +86-312-7528401 Fax: +86-312-7521279 Verticillium dahliae is a phytopathogenic fungal pathogen that causes vascular wilt diseases responsible for considerable decreases in cotton yields. Enhancing the immune system of plants is regarded as useful for controlling this disease. Lignification of cell wall appositions is a conserved basal defense mechanism in plant innate immune response. Significant roles of laccase family in cotton fiber development had been reported. However, the function of laccase involved in defense-induced lignification has not been described to date. During screening the SSH library of resistant cultivar Jimian20 inoculated by V. dahliae, a laccase gene displayed strongly induced by the pathogen, which was phylogenetically related to AtLAC15 gene, containing conserved domains that laccase commonly possessed, thus named it as GhLAC15. Overexpression GhLAC15 gene in Arabidopsis enhanced cell wall lignification, resulting in increasing the total lignin and G monolignol as well as the radio of G/S, which significantly improved the Verticillium wilt resistance of transgenic plants. In addition, the predominant carbohydrate constituents of cell wall, arabinose (Ara), xylose (Xyl) and glucose (Glc), displayed obvious difference between transgenic plants and wild type. The levels of Ara and Xyl distinctly increased, whereas the Glc level decreased in transgenic Arabidopsis. Based on the high levels of Ara and Xyl representing a high content of arabinose-substituted xylan (arabinoxylan) in enhancing plant resistance to pathogen, the high levels of Ara and Xyl provided the biochemical evidence in defense against V. dahliae in our transgenic Arabidopsis. Furthermore, suppressing the transcriptional level of GhLAC15, via virus-induced gene silencing, resulted in the increase of diseased plant rate and disease index in cotton. More fungal colonies were found in the roots of silent plants, suggesting that the extent of fungal colonization in silent plants was much more severe than in control plants. The content of monolignol and the G/S radio also decreased in the silent cotton plants, which led to resistant cotton cv. Jimian20 susceptible to the disease. These results demonstrated that GhLAC15 gene enhanced Verticillium wilt resistance via increasing defense-induced lignification and arabinose and xylose accumulation in the cell wall of G. hirsutum. This broadens our knowledge in defense-induced lignifications and cell wall modification as a defense mechanism against V. dahliae.

Cotton functional genomics promise to enhance the understanding of fundamental plant biology to systematically exploit genetic resources for improvement of cotton fibre quality and yield, as well as utilization of genetic information for germplasm improvement. However, determining the cotton gene functions is a much more challenging task which has not progressed at rapid pace. Genome sequencing technologies has been improved with exponent pace,and some species such as G.raimondii, G.arborem, G.hirsutum,G.barbadense have been sequenced. but precise chromosome-scale assembling of genomes remained an important challenge.This paper presents a comprehensive overview on the recent tools and resources available with the major advances of cotton functional genomics to develop elite cotton genotypes ,and we generated significantly correct high quality assembly of G. arboreum single chromosome by genetic map and reference assisted approaches.

Cotton not only provides the largest renewal source of textile fiber, but also is a model for studying fiber cell differentiation, cellulose biosynthesis, as well as polyploidy and its impact on genome evolution and crop domestication. In this report, we will update the progress of collective efforts on generating reference-grade sequences of the tetraploid cotton genomes and analyzing the structure and function of these genomes using multi-dimensional and integrated approaches.