Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

Weibo Xie, Qi Feng, Huihui Yu, Xuehui Huang, Qiang Zhao, Yongzhong Xing, Sibin Yu, Bin Han, and Qifa Zhang

National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China

Abstract: Bar-coded multiplexed sequencing approaches based on new-generation sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. However, such approaches usually generate low-coverage and error-prone sequences for each line in a population. Thus, it is a significant challenge to genotype individual lines in a population for linkage map construction based on low-coverage sequences without the availability of high-quality genotype data of the parental lines. In this paper, we report a method for constructing ultrahigh-density linkage maps composed of high-quality single-nucleotide polymorphisms (SNPs) based on low-coverage sequences of recombinant inbred lines. First, all potential SNPs were identified to obtain drafts of parental genotypes using a maximum parsimonious inference of recombination, making maximum use of SNP information found in the entire population. Second, high-quality SNPs were identified by filtering out low-quality ones by permutations involving resampling of windows of SNPs followed by Bayesian inference. Third, lines in the mapping population were genotyped using the high-quality SNPs assisted by a hidden Markov model. With 0.05× genome sequence per line, an ultrahigh-density linkage map composed of bins of high-quality SNPs using 238 recombinant inbred lines derived from a cross between two rice varieties was constructed. Using this map, a quantitative trait locus for grain width (GW5) was localized to its presumed genomic region in a bin of 200 kb, confirming the accuracy and quality of the map. This method is generally applicable in genetic map construction with low-coverage sequence data.

Genetic and Molecular Basis of Rice Yield

Xing Y, Zhang Q

National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan,430070 China.

Abstract: Grain yield in rice is a complex trait multiplicatively determined by its three component traits: number of panicles, number of grains per panicle, and grain weight, all of which are typical quantitative traits. The developments in genome mapping, sequencing, and functional genomic research have provided powerful tools for investigating the genetic and molecular bases of these quantitative traits. Dissection of the genetic bases of the yield traits based on molecular marker linkage maps resolved hundreds of quantitative trait loci (QTLs) for these traits. Mutant analyses and map-based cloning of QTLs have identified a large number of genes required for the basic processes underlying the initiation and development of tillers and panicles, as well as genes controlling numbers and sizes of grains and panicles. Molecular characterization of these genes has greatly advanced the mechanistic understanding of the regulation of these rice yield traits. These findings have significant implications in crop genetic improvement.

Erratum to: Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice

Hu H, You J, Fang Y, Zhu X, Qi Z, Xiong L

National Center of Plant Gene Research (Wuhan), National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.

Systematic analysis of GT factor family of rice reveals a novel subfamily involved in stress responses

Fang Y, Xie K, Hou X, Hu H, Xiong L

National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070, Wuhan, China.

Abstract: GT factors constitute a plant-specific transcription factor family with a conserved trihelix DNA-binding domain. In this study, comprehensive sequence analysis suggested that 26 putative GT factors exist in rice. Phylogenetic analysis revealed three distinctive subfamilies (GTalpha, GTbeta, and GTgamma) of plant GT factors and each subfamily has a unique composition of predicted motifs. We characterized the OsGTgamma-1 gene, a typical member of the GTgamma subfamily in rice. This gene encodes a protein containing a conserved trihelix domain, and the OsGTgamma-1:GFP fusion protein was targeted to nuclei of rice cells. The transcript level of OsGTgamma-1 was strongly induced by salt stress and slightly induced by drought and cold stresses and abscisic acid treatment. Two other members of the GTgamma subfamily, OsGTgamma-2 and OsGTgamma-3, were also induced by most of the abiotic stresses. These results suggested that the genes of the GTgamma subfamily in rice may be involved in stress responses. A homozygous mutant osgtgamma-1 (with T-DNA inserted in the promoter region of OsGTgamma-1) showed more sensitive to salt stress than wild-type rice. Overexpression of OsGTgamma-1 in rice enhanced salt tolerance at the seedling stage. This evidence suggests that the OsGTgamma subfamily may participate in the regulation of stress tolerance in rice.

Hybrid sterility in plant: stories from rice

Ouyang Y, Liu YG, Zhang Q

National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.

Abstract: Hybrid sterility is the most common form of postzygotic reproductive isolation in plants. The best-known example is perhaps the hybrid sterility between indica and japonica subspecies of Asian cultivated rice (Oryza sativa L.). Major progress has been reported recently in rice in identifying and cloning hybrid sterility genes at two loci regulating female and male fertility, respectively. Genetic analyses and molecular characterization of these genes, together with the results from other model organisms especially Drosophila, have advanced the understanding of the processes underlying reproductive isolation and speciation. These findings also have significant implications for crop genetic improvement, by providing the feasibility and strategies for overcoming intersubspecific hybrid sterility thus allowing the development of intersubspecific hybrids.