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Haplotype Diversity at Sub1 Locus and Allelic Distribution Among rice Varieties of Tide and Flood Prone Areas of South-East Asia

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rice science 2017年第4期24卷 198-206页

作者： A.S.M.MASUDUZZAMAN Md.Maksudul HAQUE A.K.M.SHAMSUDDIN M.A.SALAM Md.Ansar ALI Plant breeding division Bangladesh Rice Research InstituteGazipur 1701Bangladesh Scientific Officer(Golden rice) Plant Breeding DivisionBangladesh Rice research InstituteGazipur 1701Bangladesh Department of Genetics and Plant breeding Bangladesh Agricultural UniversityMymensingh 2202Bangladesh Director Research Bangladesh Rice Research InstituteGazipur 1701Bangladesh

Single nucleotide polymorphisms and restriction digestion-based haplotype variations among 160 flood prone rice varieties were analyzed with enzymes Alu I and Cac8 I to generate polymorphisms at Sub1A and Sub1C loci （conferring submergence tolerance）, respectively. Haplotype associated with phenotype was used to study the haplotype variations at Sub1A and Sub1C loci and to determine their functional influence on submergence tolerance and stem elongation. Three patterns at Sub1A locus, Sub1A0 （null allele）, Sub1A1 （does not cut） and Sub1A2 （one SNP）, and four patterns at Sub1C locus, Sub1C1, Sub1C2, Sub1C3 and Sub1C4, were generated. Both tolerant Sub1A1 and intolerant Sub1A2 had the same length, but the difference was presence of a restriction site in the Sub1A2, but absent at the Sub1A1. Further, two types of polymorphism were detected at the Sub1C, one included major length polymorphisms （165, 170 and 175 bp） and the other was a single restriction site at different position. Eight haplotypes （different combinations of the two loci）, A1C1, A1C2, A1C4, A2C2, A2C4, A0C2, A0C3 and A0C4, were detected among 160 varieties. Haplotype A1C1 was comparatively more related to haplotypes A1C2 and A1C4, having the same Sub1A allele, and these haplotypes were found only in Bangladeshi, Sri Lankan and Indian varieties. Most tolerant varieties in A1C1 haplotype showed slow elongation, having tolerant specific Sub1A1 and Sub1C1 alleles. Further, the varieties Madabaru and Kottamali （A2C2） also showed moderate level of tolerance without Sub1A1 allele. These varieties were different with FR13A and also suspected to carry different novel tolerant genes at other loci. These materials could be used for hybridization with Sub1 varieties for pyramiding additional tolerant specific alleles into a single genotype for improving submergence tolerance in rice.

关键词： haplotype Sub1 allele single nucleotide polymorphism submergence

Morphological and Genetical Variability among Rhizoctonia solani Isolates Causing Sheath Blight Disease of rice

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rice science 2016年第1期23卷 42-50页

作者： Zakiah Rahman MONI Md Ansar ALI Md Shahidul ALAM Md Asif RAHMAN Md Rejwan BHUIYAN Md Salim MIAN Khandakar Md IFTEKHARUDDAULA Md Abdul LATIF Mohammad Ashik Iqbal KHAN Plant breeding division Bangladesh Rice Research Institute Director Research Bangladesh Rice Research Institute Department of Botany Rajshahi University Department of Genetics and Plant breeding Bangabandhu Sheikh Mujibur Rahman Agricultural University Plant Pathology division Bangladesh Rice Research Institute

Eighteen isolates of Rhizoctonia solani collected from infected rice plants in four different locations of Bangladesh were studied by using morphological characters and molecular markers. Anastomosis study with a reference isolate confirmed that all the isolates belonged to R. solani. Significant variation was observed in sclerotial size, shape and distribution. Un-weighted pair group method with arithmetic mean dendrogram constructed based on the Gower＇s general similarity coefficient showed that these isolates were grouped into four clusters at the 0.68 similarity coefficent according to morphological characters. Cluster I was a major cluster consisting of 13 isolates, while clusters Ⅱ to Ⅳ consisted of 1 or 2 isolates. Analyses by variable number of tandem repeat and amplified fragment length polymorphism markers showed that the isolates were grouped into five and three clusters at a similarity coefficient of 0.64 and 0.69, respectively. Although most of the variability was found between isolates from different regions as expected, significant variation was observed within the isolates collected from similar agro-ecological regions. Our results suggest the presence of different races of R. solani within the same local geographic regions.

关键词： rice Rhizoctonia solani fungal variability molecular marker morphological character

Yield Traits and Associated Marker Segregation in Elite Introgression Lines Derived from O. sativa × O. nivara

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rice science 2018年第1期25卷 19-31页

作者： G.HARITHA B.P.M.SWAMY M.L.NAIK B.JYOTHI B.DIVYA S.MALATHI N.SARLA Indian Council of Agricultural Research Indian Institute of Rice Research Plant breeding Genetics and Biotechnology Division International Rice Research Institute

Introgression lines(ILs)derived from interspecific crosses are a source of new genetic variability.A total of 55 ILs derived from two crosses Swarna×*** IRGC81848(population A)and Swarna×*** IRGC81832(population B)were characterized for yield and yield-related traits/*** of 103 simple sequence repeat(SSR)markers associated with yield-related QTLs was *** A showed an average of 12.6%homozygous *** alleles and population B showed 10.6%.Interestingly,three SSR markers,RM223,RM128 and RM517,showed conspicuous pattern of *** distribution of parental alleles at three loci RM223,RM128 and RM517 linked to yield-related traits was *** markers flanked to several yield-related ***223,flanking to qyld8.3,was heterozygous in almost all the 55 ILs except in IL10-3S and ***128 on chromosome 1 and RM517 on chromosome 3 were mutually exclusive in 46 out of 55 *** 46 ILs showed either of the marker allele RM128 or RM517 from *** but not ***166S had both RM128and RM517 from *** and the other ILs showed homozygous Swarna allele at RM517 except *** structure assigned the 55 ILs to three sub-populations based on their genomic ***65S,IL166S,IL248S,IL7K and IL250K showed high yields in multi-location trials,and IL248S was released for cultivation as DRRDhan 40.

关键词： introgression line heterozygosity Oryza nivara wild rice population structure yield simple sequence repeat

Natural Variation of Leaf Thickness and Its Association to Yield Traits in indica rice

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Journal of Integrative Agriculture 2014年第2期13卷 316-325页

作者： LIU Chuan-guang ZHOU Xin-qiao CHEN Da-gang LI Li-jun LI Ju-chang CHEN You-ding rice Research Institute Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding

Leaf thickness is an important morphological trait in rice. Its association to the yield potential, as of now has not been documented because of the shortage of the equipment which could conveniently measure the leaf thickness in rice. In this study, the thickness of top three leaves of 208 cultivars had been determined by a nondestructive rice leaf thickness instrument for the research of the natural variation of leaves thickness and its association to yield traits in indica rice. The results showed that the flag leaf was the thickest, and the 2nd leaf was thicker than the 3rd leaf. Analysis of variance indicated the existence of wide genetic diversity of leaf thickness among the investigated indica rice genotypes. The tight correlation among the thicknesses of the top three leaves means that the leaf thickness traits share one genetic control system. Leaf thickness had a significant positive correlation with leaf length and a positive correlation with leaf width, indicated that thicker leaf was beneficial to increasing the single leaf area. The results of correlation analysis revealed that thicker leaf should be profitable to the leaf erection, higher numbers of grains per panicle and higher grains weight per panicle. However, the significantly negative correlation between leaf thickness and number of panicles per plant counteracted the profitability from increased grains weight per panicle, so that the correlations of the thicknesses of the top three leaves to yield and biomass were positive but not significantly. It has made great progress in the genetic improvement of leaves thickness in inbred indica rice breeding in Guangdong Province, China, since the 1990s.

关键词： indica rice leaf thickness variation yield

Phenotype of rice Floury Endosperm Mutant flo7 and Fine Mapping of Mutated Gene

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rice science 2015年第4期22卷 162-170页

作者： SHENG Zhong-hua FANG Peng-fei LI San-feng JIAO Gui-ai XIE Li-hong HU Pei-song TANG Shao-qing WEI Xiang-jin State Key Laboratory of rice Biology/Key Laboratory of rice Biology and Genetic breeding of Ministry of Agriculture China National Rice Research Institute

The major storage substance in rice endosperm is starch, which accounts for 80% of dry matter weight. In this study, rice mutant flo7, selected from the progeny of Nipponbare＇s tissue culture, displayed floury and opaque endosperm. Compared with its corresponding wild type （WT） Nipponbare, the mutant rio7 produced longer, narrower, thinner and lighter grains. The levels of glucose, fructose and sucrose in the mutant flo7 endosperm were higher than those in the WT endosperm, whereas the protein content was not affected. With respect to both amylose content and gel consistency, the mutant flo7 was lower than WT, but its alkali value was higher. Scanning electron microscopic examinations showed that the endosperm of the mutant flo7 contained irregular, loosely packed and compound starch granules. Genetic analysis indicated that the mutant phenotype was determined by a single recessive nuclear gene The flo7 locus was mapped to a region on the long arm of chromosome 12, within a 95.1 kb interval defined by the markers C2-11 and C5-15. There are 13 open reading frames in the mapping interval. Transcription profiling of the developing grains showed that a number of genes involved in starch synthesis were affected differently in the mutant flo7.

关键词： flo7 floury endosperm starch fine mapping rice mutant

Comparison and analysis of QTLs for grain and hull thickness related traits in two recombinant inbred line(RIL) populations in rice(Oryza sativa L.)

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Journal of Integrative Agriculture 2016年第11期15卷 2437-2450页

作者： YAO Xiao-yun WANG Jia-yu LIU Jin WANG Wei YANG Sheng-long ZHANG Yu XU Zheng-jin Key Laboratory of Northeast rice Biology and breeding Ministry of Agriculture/Rice Research InstituteShenyang Agricultural University

Grain traits are major constraints in rice production, which are key factors in determining grain yield and market values. This study used two recombinant inbred line（RIL） populations, RIL-JJ（japonica/japonica） and RIL-IJ（indica/japonica） derived from the two crosses Shennong 265/Lijiangxintuanheigu（SN265/LTH） and Shennong 265/Luhui 99（SN265/LH99）. Sixty-eight quantitative trait loci（QTLs） associated with 10 grain traits were consistently detected on the 12 chromosomes across different populations and two environments. Although 61.75% of the QTLs clustered together across two populations, only 16.17% could be detected across two populations. Eight major QTLs were detected on the 9, 10 and 12 chromosomes in RIL-JJ under two environments, a novel QTL clustered on the 10 chromosome, q GT10, q BT10 and q TGW10, have a higher percentage of explained phenotypic variation（PVE） and additive effect; 15 major QTLs were detected on the 5, 8, 9, and 11 chromosomes in RIL-IJ under two environments, a novel clustered QTL, q GT8 and q TGW8, on the 8 chromosome have a higher additive effect. Finally, the analysis of major QTL-BSA mapping narrowed the q TGW10 to a 1.47-Mb region flanked by simple sequence repeat markers RM467 and RM6368 on chromosome 10. A comparison of QTLs for grain traits in two different genetic backgrounds recombinant inbred line populations confirmed that genetic background had a significant impact on grain traits. The identified QTLs were stable across different populations and various environments, and 29.42% of QTLs controlling grain traits were reliably detected in different environments. Fewer QTLs were detected for brown rice traits than for paddy rice traits, 7 and 17 QTLs for brown rice out of 25 and 43 QTLs under RIL-JJ and RILIJ populations, respectively. The identification of genes constituting the QTLs will help to further our understanding of the molecular mechanisms underlying grain shape.

关键词： paddy rice brown rice hull thickness genetic backgrounds QTL mapping rice (Oryza sativa L.)

Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015's Responses Against Brown Planthopper Infestation

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rice science 2024年第3期31卷 317-327,I0042-I0045页

作者： LI Dian DUAN Wenjing LIU Qun’en WU Weixun ZHAN Xiaodeng SUN Lianping ZHANG Yingxin CHENG Shihua State Key Laboratory of rice Biology and breeding China National Rice Research InstituteHangzhou 310006China

Accurate genomic information is essential for advancing genetic breeding research in specific rice *** study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene ***,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)*** transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH *** analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall *** results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid *** association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH *** summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.

关键词： brown planthopper gapless genome genome assembly multi-omics Nilaparvata lugens rice

Carbon Catabolite Repressor UvCreA is Required for Development and Pathogenicity in Ustilaginoidea virens

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rice science 2024年第2期31卷 203-214,I0029-I0031页

作者： XIE Shuwei SHI Huanbin WEN Hui LIU Zhiquan QIU Jiehua JIANG Nan KOU Yanjun State Key Laboratory of rice Biology and breeding China National Rice Research InstituteHangzhou 311400China

The rice false smut disease, caused by Ustilaginoidea virens, has emerged as a significantglobal threat to rice production. The mechanism of carbon catabolite repression plays a crucial role in theefficient utilization of carbon nutrients and enzyme regulation in the presence of complex nutritionalconditions. Although significant progress has been made in understanding carbon catabolite repression infungi such as Aspergillus nidulans and Magnaporthe oryzae, its role in U. virens remains unclear. Toaddress this knowledge gap, we identified UvCreA, a pivotal component of carbon catabolite repression,in U. virens. Our investigation revealed that UvCreA localized to the nucleus. Deletion of UvCreA resultedin decreased growth and pathogenicity in U. virens. Through RNA-seq analysis, it was found that theknockout of UvCreA led to the up-regulation of 514 genes and down-regulation of 640 genes. Moreover,UvCreA was found to be involved in the transcriptional regulation of pathogenic genes and genesassociated with carbon metabolism in U. virens. In summary, our findings indicated that UvCreA isimportant in fungal development, virulence, and the utilization of carbon sources through transcriptionalregulation, thus making it a critical element of carbon catabolite repression.

关键词： Ustilaginoidea virens virulence carbon catabolite repression Oryza sativa rice false smut

ORYZA SATIVA SPOTTED-LEAF 41(OsSPL41) Negatively Regulates Plant Immunity in rice

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rice science 2023年第5期30卷 426-436,I0017-I0020页

作者： TAN Jingyi ZHANG Xiaobo SHANG Huihui LI Panpan WANG Zhonghao LIAO Xinwei XU Xia YANG Shihua GONG Junyi WU Jianli State Key Laboratory of rice Biology and breeding China National Rice Research InstituteHangzhou 310006China

Identification of immunity-associated leucine-rich repeat receptor-like protein kinases(LRR-RLK) is critical to elucidate the LRR-RLK mediated mechanism of plant ***,we reported the map-based cloning of a novel rice SPOTTED-LEAF 41(Os SPL41) encoding a putative LRR-RLK protein(Os LRR-RLK41/Os SPL41) that regulated disease responses to the bacterial blight pathogen Xanthomonas oryzae ***(Xoo).An 8-bp insertion at position 865 bp in a mutant spotted-leaf 41(spl41) allele led to the formation of purple-brown lesions on *** complementation by the wild type allele(Os SPL41) can rescue the mutant phenotype,and the complementary lines showed similar performance to wild type in a number of agronomic,physiological and molecular *** SPL41 was constitutively expressed in all tissues tested,and Os SPL41 contains a typical transmembrane domain critical for its localization to the cell *** mutant exhibited an enhanced level of resistance to Xoo in companion of markedly up-regulated expression of pathogenesis-related genes such as Os PR10a,Os PAL1 and Os NPR1,while the level of salicylic acid was significantly increased in *** contrast,the over-expression lines exhibited a reduced level of H_(2)O_(2) and were much susceptible to Xoo with down-regulated expression of pathogenesis-related *** results suggested that Os SPL41 might negatively regulate plant immunity through the salicylic acid signaling pathway in rice.

关键词： bacterial blight leucine-rich repeat receptor-like protein kinase plant immunity reactive oxygen species rice spotted leaf