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Fixation of hybrid sterility genes and favorable alleles of key yield-related genes with dominance contribute to the high yield of the Yongyou series of intersubspecific hybrid rice

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Journal of Genetics and Genomics 2022年第5期49卷 448-457页

作者： Pengfei Wang Feixiang Qi Honglin Yao Xingbing Xu Wenjun Li Jianghu Meng Qinglu Zhang weibo xie Yongzhong Xing National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhanHubei 430070China Hubei Hongshan Laboratory WuhanHubei 430070China

In rice,the Yongyou series of Xian-Geng intersubspecific hybrids have excellent production performance,as shown by their extremely high yield.However,the mechanisms underlying the success of these rice hybrids are unclear.In this study,three F2 populations are generated from three Yongyou hybrids to determine the genetic basis of the extremely high yield of intersubspecific hybrids.Genome constitution analysis reveals that the female and male parental lines belong to the Geng and Xian subspecies,respectively,although introgression of 20%of the Xian ancestry and 14%of the Geng ancestry are observed.Twenty-five percent of the hybrid genomes carries homozygous Xian or Geng fragments,which harbors hybrid sterility genes such as Sd,Sc,f5,and q S12 and favorable alleles of key yield-related genes,including NAL1,Ghd7,and Ghd8.None of the parents carries the S5+killer of the S5 killer-protector system.Compatible allele combinations of hybrid sterility genes ensure the fertility of these intersubspecific hybrids and overcome the bottleneck in applying intersubspecific hybrids.Additive effects of favorable alleles of yield-related genes fixed in both parents enhances midparent values.Many QTLs for yield and its key component spikelets per panicle shows dominance and the net positive dominant effects lead to heterosis.These factors result in an extremely high yield of the hybrids.These findings will aid in the development of new intersubspecific rice hybrids with diverse genetic backgrounds.

关键词： Intersubspecific hybrid Heterosis Fertility Introgression Favorable alleles Dominance

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RNA-Directed DNA Methylation Is Involved in Regulating Photoperiod-Sensitive Male Sterility in Rice

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Molecular Plant 2012年第6期5卷 1210-1216页

作者： Jihua Ding Jianqiang Shen Hailiang Mao weibo xie Xianghua Li Qifa Zhang National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research(Wuhan) I-luazhong Agriculture UniversityWuhan 430070China

Photoperiod-sensitive male sterility （PSMS） is a valuable germplasm for hybrid rice breeding. Recently, we cloned pros3, a locus controlling PSMS, which encodes a long non-coding RNA called LDMAR required for normal male fertility of the rice plant under long-day conditions. Increased methylation in the promoter of LDMAR in the PSMS rice （Nongken 58S） relative to the wild-type （Nongken 58） reduced expression of LDMAR leading to male sterility under long-day conditions. In this study, we identified a siRNA named Psi-LDMAR in the LDMAR promoter region that was more abundant in Nongken 58S than in Nongken 58. We showed that Psi-LDMAR was likely derived from AKl11270, a transcript obtained from the sense strand of the LDMAR promoter with its 3＇-end having a 110-base overlap with the 5＇-end of LDMAR. Overexpressing AKl11270 in Nongken 58S greatly enriched Psi-LDMAR, which induced RNA-directed DNA methylation in the LDMAR promoter and repressed the expression of LDMAR. Reduction of LDMAR in Nongken 58S changed the critical day length for fertility recovery and delayed the fertility recovery under short-day conditions. This result added to our understanding of the molecular mechanism for PSMS.

关键词： Oryza sativa siRNA Psi-LDMAR epigenetics hybrid rice.

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Natural Variation in the Sequence of SNAC1 and Its Expression Level Polymorphism in Rice Germplasms under Drought Stress

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Journal of Genetics and Genomics 2014年第11期41卷 609-612页

作者： Khamdok Songyikhangsuthor Zilong Guo Nili Wang Xiaoyi Zhu weibo xie Tongmin Mou Lizhong Xiong National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University

Water is a major limiting factor for food production and many countries fail to produce sufficient food for their population due to severe water scarcity （Jury and Vaux, 2005）. Rice is the main staple food worldwide. More than 50% of rice in the world is rain-fed and drought causes severe reduction in rice grain yield in rain-fed environments （Venuprasad et al., 2007; Zhang, 2007; Sandhu et al., 2014）. Therefore, enhancing drought resistance （DR） of rice is important for food security. However, DR is a complex trait, which is controlled by a large number of loci with small effect and is also affected by different genetic background, genotype-by-environment interaction and other stresses such as heat （Hu and Xiong, 2014）.

关键词： SNAC Natural Variation in the Sequence of SNAC1 and Its Expression Level Polymorphism in Rice Germplasms under Drought Stress

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QTL Scanning for Rice Yield Using a Whole Genome SNP Array

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Journal of Genetics and Genomics 2013年第12期40卷 629-638页

作者： Cong Tan Zhongmin Han Huihui Yu Wei Zhan weibo xie Xun Chen Hu Zhao Fasong Zhou Yongzhong Xing National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene ResearchHuazhong Agricultural University Life Science and Technology Center China National Seed Group Co.Ltd.

High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line （RIL） population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length ofl.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.

关键词： RILs RICE6K SNP array Bin map Segregation distortion QTL

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Genome-and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

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Molecular Plant 2021年第3期14卷 470-487页

作者： Shan Tang Hu Zhao Shaoping Lu Liangqian Yu Guofang Zhang Yuting Zhang Qing-Yong Yang Yongming Zhou Xuemin Wang Wei Ma weibo xie Liang Guo National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhanChina Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhanChina Department of Biology University of Missouri-St.LouisSt.LouisMO 63121USA Donald Danforth Plant Science Center St.LouisMO 63132USA School of Biological Sciences Nanyang Technological UniversitySingapore 637551Singapore

Seed oil content(SOC)is a highly important and complex trait in oil crops.Here,we decipher the genetic basis of natural variation in SOC of Brassica napus by genome-and transcriptome-wide association studies using 505 inbred lines.We mapped reliable quantitative trait loci(QTLs)that control SOC in eight environments,evaluated the effect of each QTL on SOC,and analyzed selection in QTL regions during breeding.Six-hundred and ninety-two genes and four gene modules significantly associated with SOC were identified by analyzing population transcriptomes from seeds.A gene prioritization framework,POCKET(prioritizing the candidate genes by incorporating information on knowledge-based gene sets,effects of variants,genome-wide association studies,and transcriptome-wide association studies),was implemented to determine the causal genes in the QTL regions based on multi-omic datasets.A pair of homologous genes,BnPMT6s,in two QTLs were identified and experimentally demonstrated to negatively regulate SOC.This study provides rich genetic resources for improving SOC and valuable insights toward understanding the complex machinery that directs oil accumulation in the seeds of B.napus and other oil crops.

关键词： Brassica napus seed oil content QTL GWAS TWAS gene module

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An inferred functional impact map of genetic variants in rice

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Molecular Plant 2021年第9期14卷 1584-1599页

作者： Hu Zhao Jiacheng Li Ling Yang Gang Qin Chunjiao Xia Xingbing Xu Yangmeng Su Yinmeng Liu Luchang Ming Ling-Ung Chen Lizhong Xiong weibo xie National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhanChina State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanningChina

Interpreting the functional impacts of genetic variants(GVs)is an important challenge for functional genomic studies in crops and next-generation breeding.Previous studies in rice(Oryza sativa)have focused mainly on the identification of GVs,whereas systematic functional annotation of GVs has not yet been performed.Here,we present a functional impact map of GVs in rice.We curated haplotype information for 17397026 GVs from sequencing data of 4726 rice accessions.We quantitatively evaluated the effects of missense mutations in coding regions in each haplotype based on the conservation of amino acid residues and obtained the effects of 918848 non-redundant missense GVs.Furthermore,we generated high-quality chromatin accessibility(CA)data from six representative rice tissues and used these data to train deep convolutional neural network models to predict the impacts of 5067405 GVs for CA in regulatory regions.We characterized the functional properties and tissue specificity of the GV effects and found that large-effect GVs in coding and regulatory regions may be subject to selection in different directions.Finally,we demonstrated how the functional impact map could be used to prioritize causal variants in mapping populations.This impact map will be a useful resource for accelerating gene cloning and functional studies in rice,and can be freely queried in RiceVarMap V2.0(http://***).

关键词： ricegenetic variantschromatin accessibilityfunctional impact mapdeep learning

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Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study

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Molecular Plant 2015年第6期8卷 946-957页

作者： Quanxiu. Wang weibo xie Hongkun Xing Ju Yan Xiangzhou Meng Xinglei Li Xiangkui Fu Jiuyue Xu Xingming Lian Sibin Yu Yongzhong Xing Gongwei Wang National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070China

Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photo- synthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice （Oryza sativa） and the extent of variations explored is very limited. We con- ducted a genome-wide association study （GWAS） using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demon- strated that Grain number, plant height, andheading date7 （GhdT） was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down- regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 （NAL1） corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5＇ UTR and four non-synonymous SNPs in the cod- ing region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes iden- tified would help to fine-tune and optimize the antenna size of canopies in rice breeding.

关键词： chlorophyll GWAS Ghd7 NAL 1 pleiotropic effect Oryza sativa

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Origination and Establishment of a Trigenic Reproductive Isolation System in Rice

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Molecular Plant 2016年第11期9卷 1542-1545页

作者： Yidan Ouyang Guangwei Li Jiaming Mi Conghao Xu Hongyi Du Chengjun Zhang weibo xie Xianghua Li Jinghua Xiao Huazhi Song Qifa Zhang National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070 China Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences No. 132 Lanhei Road Kunming Yunnan 650201 China These authors contributed equally to this article

Dear Editor,Reproductive isolation is both the indicator and a primary force of speciation, and plays a key role in maintaining species identity. Understanding the origin and mechanisms of reproductive isola- tion is of fundamental importance in evolutionary biology. In recent years, a number of genes that induce reproductive barriers have been identified in several model organisms such as Drosophila, rodents, yeast, Arabidopsis.

关键词：果蝇属基因理解力拟南芥属生物学稻属移民(移出和移入) 胰岛素

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Rice Information GateWay： A Comprehensive Bioinformatics Platform for Indica Rice Genomes

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Molecular Plant 2018年第3期11卷 505-507页

作者： Jia-Ming,Song Yang,Lei Cheng-Cheng,Shu Yuduan,Ding Feng,Xing Hao,Liu Jia,Wang weibo,xie Jianwei,Zhang Ling-Ling,Chen National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan 430070 P. R. China Agricultural Bioinformatics Key Laboratory of Hubei Province College of Informatics Huazhong Agricultural University Wuhan 430070 China [∗]Corresponding author [∗∗]Corresponding author

Dear Editor,Oryza sativa subsp, indica and japonica are two subspecies of Asian cultivated rice, among which indica rice is much more widely grown and genetically diverse. Over the past years, the Rice Annotation Project Database （RAP-DB）（Ohyanagi et al., 2006） and Michigan State University Rice Genome Annotation Project （MSU-RGAP）（Ouyang et al., 2007） are two popular databases that have been developed to manage rice genomic and transcriptomic data based on the unified reference genome of japonica cultivar Nipponbare （International Rice Genome Sequencing Project, 2005）. Beijing Genomics Institute Rice Information System （BGI-RIS）（Zhao et ai., 2004） is an available resource for indica rice cultivar 93-11;

关键词： SEQUENCE RESOURCE DATABASE

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A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding

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Molecular Plant 2014年第3期7卷 541-553页

作者： Haodong Chen weibo xie Hang He Huihui Yu Wei Chen Jing Li Renbo Yu Yue Yao Wenhui Zhang Yuqing He Xiaoyan Tang Fasong Zhou Xing Wang Deng Qifa Zhang Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology State Key Laboratory of Protein and Plant Gene Research College of LifeSciences Peking University Beijing 100871 China National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan430070 China Life Science and Technology Center China National Seed Group Co. Ltd Wuhan 430075 China Shenzhen Institute of Molecular Crop Design Shenzhen 518107 China Frontier Laboratories of Systems Crop Design Co. Ltd Beijing 100085 China

A high-density single nucleotide polymorphism （SNP） array is critically important for geneticists and molecu- lar breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the devel- opment of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for dif- ferent objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies （GWAS） analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.

关键词： single nucleotide polymorphisms （SNPs） array rice molecular breeding.

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