International Consortium of Rice Mutagenesis: resources and beyond

Rice is one of the most important crops in the world. The rice community needs to cooperate and share efforts and resources so that we can understand the functions of rice genes, especially those with a role in important agronomical traits, for application in agricultural production. Mutation is a major source of genetic variation that can be used for studying gene function. We will present here the status of mutant collections affected in a random manner by physical/chemical and insertion mutageneses.As of early September 2013, a total of 447, 919 flanking sequence tags from rice mutant libraries with T-DNA, Ac/Ds, En/Spm, Tos17, nDART/aDART insertions have been collected and publicly available. From these, 336,262 sequences are precisely positioned on the japonica rice chromosomes, and 67.5% are in gene interval. We discuss the genome coverage and preference of the insertion, issues limiting the exchange and use of the current collections, as well as new and improved resources. We propose a call to renew all mutant populations as soon as possible. We also suggest that a common web portal should be established for ordering seeds.     

Research Progress on Goat Genetic Diversity and Production Traits Based on High-throughput Sequencing Technology

Recently, the widespread use of high-throughput sequencing technology and the development of bioinformatics have been greatly contributed to the development of farm animal genomics. Whole genome-wide analysis can facilitate the fine mapping of the molecular markers related to the production traits quickly and accurately, thus providing an important theoretical basis for genome selection breeding. Several thousand years of domestication and artificial selection produce many modern goat breeds with high production of milk, fiber, and meat, which become abundant production and living materials for human populations. Researchers have studied the genetic diversity and molecular mechanisms of production traits in goats using high-throughput sequencing technology, in order to identify candidate genes related to the excellent germplasm reliable markers for genetic improvement. In this review, we summarized the five-year research progress on the genetic diversity and production traits of goats including fiber, milk production and reproduction traits, mainly based on high-throughput sequencing technology. This paper provides a reference for the evaluation of the excellent goat genetic resources and the investigation of production trait related genes.     

我国蔬菜作物基因组研究与分子育种

我国是世界蔬菜生产大国,也是蔬菜种子销量大国,蔬菜的育种与推广非常重要。分析了我国蔬菜育种的优势和面临的挑战,综述了蔬菜基因组学和分子育种方面的研究进展,对“十二五”期间蔬菜研究的发展进行了展望。     

Cloning and Comparative Studies of Seaweed Trehalose-6-Phosphate Synthase Genes

The full-length cDNA sequence (3219 base pairs) of the trehalose-6-phosphate synthase gene of Porphyra yezoensis (PyTPS) was isolated by RACE-PCR and deposited in GenBank (NCBI) with the accession number {"type":"entrez-nucleotide","attrs":{"text":"AY729671","term_id":"56718401","term_text":"AY729671"}}AY729671. PyTPS encodes a protein of 908 amino acids before a stop codon, and has a calculated molecular mass of 101,591 Daltons. The PyTPS protein consists of a TPS domain in the N-terminus and a putative TPP domain at the C-terminus. Homology alignment for PyTPS and the TPS proteins from bacteria, yeast and higher plants indicated that the most closely related sequences to PyTPS were those from higher plants (OsTPS and AtTPS5), whereas the most distant sequence to PyTPS was from bacteria (EcOtsAB). Based on the identified sequence of the PyTPS gene, PCR primers were designed and used to amplify the TPS genes from nine other seaweed species. Sequences of the nine obtained TPS genes were deposited in GenBank (NCBI). All 10 TPS genes encoded peptides of 908 amino acids and the sequences were highly conserved both in nucleotide composition (>94%) and in amino acid composition (>96%). Unlike the TPS genes from some other plants, there was no intron in any of the 10 isolated seaweed TPS genes.     

芸薹属作物基因组研究进展及其在育种中的意义

芸薹属是芸薹科(旧称十字花科)中最为重要的一个属,属内包含许多重要的蔬菜、油料及饲料作物。有鉴于此,几十年来人们对芸薹属栽培种基因组进行了广泛、细致而深入的研究。这些基于普通细胞学、分子细胞遗传学以及比较基因组学的研究结果不仅在宏观和微观水平上初步揭示了芸薹属不同基因组的结构及相互关系,也在芸薹属作物的传统和现代分子育种中得到了广泛应用。可以预见,芸薹属作物基因组的研究,将随着芸薹属作物的基因组测序和芸薹科植物比较基因组项目(BMAP)的开展,以及表观基因组、转录组及蛋白组研究的介入而得到进一步的深化,也必将把芸薹属作物的遗传改良推向一个新台阶。     

竹类植物基因组学发展的机遇与挑战

概述了竹类植物基因组学研究进展,包括对核酸信息的认知以及通过反向遗传学对重要性状相关基因功能的认知;分析了目前包括现代生物技术、可再生生物资源、生态文明所带来的良好发展机遇;提出了竹类植物基因组复杂、开花特殊、遗传转化体系不完善等基因组学研究所面临的瓶颈问题及其对策。     

植物功能基因组研究主要方法在茶树上的应用

随着大量基因序列的产生,植物基因组研究已从结构基因组转向功能基因组研究,随之一些新的方法和技术相继建立。茶树庞大而复杂的基因组,使得茶树功能基因组研究起步较晚,但也取得了很大的进步。本文就茶树在应用这些新技术研究功能基因组所取得的进展和突破进行概述。     

乳酸菌基因组学研究进展

乳酸菌基因组学的研究有助于揭示乳酸菌的遗传和代谢机制,通过分析相关功能基因与益生功能的联系,能够充分发挥乳酸菌应用潜力。作者就乳酸菌基因组基本特征、代谢特点、重要功能基因、乳酸菌的比较基因组学进行了综述。     

禾草内生真菌研究及应用进展

内生真菌感染大部分禾草形成互惠共生体,提高共生体对环境适应性,并进而对动物、微生物以及整个生态系统产生广泛的影响,使该领域成为近年来研究的热点问题。分子生物学技术、基因组学、蛋白组学和代谢组学以及相应的信息生物学技术的应用加快了禾草内生真菌的研究,尤其是内生真菌全基因组序列的测定,明确了次生代谢物多样性及其与基因的关系,鉴定相关的功能基因和蛋白,基因敲除技术阐释了维持内生真菌与寄主动态平衡的分子机制。利用基因组学等技术筛选对家畜无毒的内生真菌菌株, 通过接种技术建立新的既具有抗逆性,又对家畜无毒的禾草-内生真菌共生体,提高禾草的品质并确保对动物的安全性,在牧草及草坪草育种上获得了巨大成功。但是内生真菌的寄主特异性限制了内生真菌可利用的范围,因此后续应继续利用基因组学和代谢组学新技术深入研究内生真菌与寄主相互作用的机制,利用基因工程技术人工创造无毒菌株,克服共生体创制的瓶颈。本研究旨在对以上内容进行综述,以期为更广泛利用内生真菌进行牧草和草坪草育种奠定基础。     

Functional Genomics of the Aeromonas salmonicida Lipopolysaccharide O-Antigen and A-Layer from Typical and Atypical Strains

The A. salmonicida A450 LPS O-antigen, encoded by the wb_salmo gene cluster, is exported through an ABC-2 transporter-dependent pathway. It represents the first example of an O-antigen LPS polysaccharide with three different monosaccharides in their repeating unit assembled by this pathway. Until now, only repeating units with one or two different monosaccharides have been described. Functional genomic analysis of this wb_salmo region is mostly in agreement with the LPS O-antigen structure of acetylated l-rhamnose (Rha), d-glucose (Glc), and 2-amino-2-deoxy-d-mannose (ManN). Between genes of the wb_salmo we found the genes responsible for the biosynthesis and assembly of the S-layer (named A-layer in these strains). Through comparative genomic analysis and in-frame deletions of some of the genes, we concluded that all the A. salmonicida typical and atypical strains, other than A. salmonicida subsp. pectinolytica strains, shared the same wb_salmo and presence of A-layer. A. salmonicida subsp. pectinolytica strains lack wb_salmo and A-layer, two major virulence factors, and this could be the reason they are the only ones not found as fish pathogens.