Chinese Science Bulletin © 2007 SCIENCE IN CHINA PRESS Springer

www.scichina.com www.springerlink.com Chinese Science Bulletin | January 2007 | vol. 52 | no. 1 | 1-5 ARTICLES

CROP BREEDING A brief summary of major advances in cotton functional genomics and molecular breeding studies in China

Qin YongMei1 & Zhu YuXian1,2† 1 National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing,

100871, China; 2 National Center for Plant Gene Research (Beijing), Beijing100101, China

Cotton fibers, commonly known as cotton lint, are single-celled trichomes derived from epidermal lay-ers of cotton ovules. Despite of its importance in word trade, the molecular mechanisms of cotton fiber production is still poorly understood. Through transcriptome profiling, functional genomics, pro-teomics, metabolomics approaches as well as marker-assisted molecular breeding, scientists in China have made significant contributions in cotton research. Here, we briefly summarize major progresses made in Chinese laboratories, and discuss future directions and perspectives relative to the develop-ment of this unique crop plant.

Gossypium, cotton fiber, functional genomics, gene cloning, molecular breeding

Cotton accounts for about one half of the world’s natural fibers and is one of the most important economic crops in China. The Ministry of Science and Technology of the People’s Republic of China (MOST) initiated cotton functional genomics research through the High-Tech- nology Research and Development of China (“863”) in 1997 and through the “industrialization of transgenic plants” program in 1999. More recently, MOST initiated a project in the National Basic Research Program of China (973) to support the research aiming for the im-provement of both cotton lint production and fiber qual-ity. Indeed, among the 2469 research articles published in PubMed accessed journals in the last 5 years (2003—2007) that concentrated on cotton sciences, 340 were contributed by Chinese laboratories (Table 1). We thus hold a very strong second position only to United States of America which published 783 in the same period of time, in a close concert with the country being world’s number one cotton producer and manufacturer. Gossypium hirsutum and G. barbadense are natural cotton species that are allopolyploids. G. hirsutum, up-land cotton, accounts for about 92% to 95% of the an-nual cotton production in the world and generally grow

Table 1 Ranking of countries by number of articles published in PuB-Med accessed journals in last 5 years (2003―2007) with cotton as the main subject Country No. of publications USA 783 China 340 Japan 160 India 131 Australia 93 UK 83 France 51 Italy 44

up to 30―40 mm in length, about 15 μm in thickness at full maturity. G. barbadense, Sea Island cotton, repre-sents another 5% of cotton production. To fully under-stand the problem, our lab at Peking University per-formed a PCR-selected cDNA subtractive analysis using cDNAs prepared from upland cotton fiber as the testers and cDNAs from the fuzzless-lintless (fl) mutant[1] as

Received September 0, 2007; accepted October 19, 2007 doi: †Corresponding author (email: zhuyx@water.pku.edu.cn) Supported by the National Basic Research Program of China (Grant No. 2004CB117302) 2 QIN YongMei et al. Chinese Science Bulletin | Ja 2007 | vol. 52 | no. ? | 1-5

drivers, and showed that a great number of cotton genes were differentially expressed during different growth stages of the fiber[2]. We have since randomly sequenced a total of 102000 cotton ESTs (expressed sequence tags) from 0―10 days post-anthesis (dpa) cotton fiber cDNA library that accounted for about 1/3 of the cotton ESTs in GenBank databases and obtained 30154 UniESTs. As-sembly and in-depth microarray analysis of the first 12233 UniESTs revealed that more than 778 genes were specifically unregulated during fiber development[3]. Chen XiaoYa and colleagues[4] at the Institute of Plant Physiology and Ecology, Chinese Academy of Science (IPPE, CAS), have identified 633 genes that were dif-ferentially regulated during the same period of time through comparative transcriptome analysis. Similar work has been reported from Zhang Xianlong’s lab at Huazhong Agricultural University. They obtained 455 G. barbadense genes and found that almost 50% of them belong to metabolically functional categories[5], and suggested that many of these genes were associated with cotton somatic embryogenesis[6]. Metabolite profiles of cotton fiber cells provided by Chen Xiaoya’s group in-dicated that cellulose biosynthesis, cell wall-loosening and lipid biosynthesis were highly active during fiber elongation, which is consistent with transcriptome and proteomic data reported from other labs in China and around the world as well[3,4,7]. Liu JingYuan and colleagues[8,9] at Tsinghua Univer-sity developed a protocol for protein extraction from cotton fibers, which gave a higher yield, greater resolu-tion and spot intensities during subsequent two-dimen- sional electrophoresis. Our lab also performed compara-tive proteomic analysis using 10-dpa wild-type cotton ovules with fibers attached and fl mutant ovules that produced absolutely no fiber. A total of 1240 ± 20 pro-tein spots were detected on both gels and among them, 61 were either highly up-regulated or down-regulated[7]. 1 Gene cloning and functional analysis Fiber development can be divided into four develop-mental stages: (1) initiation, (2) elongation, (3) secon-dary cell wall thickening, (4) dehydration. The produc-tivity as well as the quality of cotton lint depended mainly on fiber initiation and fiber elongation since ap-proximately only 30% of the ovule epidermis develops to fiber. The initiation of a fiber cell was found devel-opmentally similar to that of the Arabidopsis trichome. Genes specifically expressed in developing cotton fiber cells encoded several transcription factors with similari-ties to the regulators of Arabidopsis trichomes[10]. For example, Chen XiaoYa[11] and colleagues found that a MYB gene (GaMYB2) from G. hirsutum, a homologue of AtGL1 encoding the Arabidopsis transcription factor R2R3 MYB, was able to rescue the Arabidopsis gl1 mutant and the expression of this cotton gene induced trichome formation on Arabidopsis seeds. Similar results were obtained from Xue YongBiao[12] in the Institute of