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Revealing Genetic Relationship and Prospecting of Novel Donors Among Upland Rice Genotypes Using qDTY-Linked SSR Markers

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Rice science 2018年第6期25卷 308-319页

作者： Mitadru MUKHERJEE Barada PADHY Bharathkumar SRINIVASAN Pradosh MAHADANI Sk Yasin BAKSH Ravindra DONDE Onkar Nath SINGH Lambodar BEHERA Padmini SWAIN Sushanta Kumar DASH crop improvement division ICAR-National Rice Research Institute Departement of Botany Kandaswamy Kandar’s College crop Physiology and Biochemistry division National Rice Research Institute

A total of 17 simple sequence repeat(SSR) markers linked to QTLs(qDTYs) governing grain yield under reproductive stage(RS) drought stress were used to assess the genetic relationship and prospecting new donors for q DTYs among 32 popular upland rice genotypes. These SSR markers generated a total of 36 alleles with an average allele count of 2.1 per locus. Polymorphic information content value of the markers ranged from 0.376 to 0.662 with an average value of 0.484. The expected heterozyogosity ranged from 0.381 to 0.632. STRUCTURE analysis divided the 32 genotypes into three sub-populations. Subsequent phenotyping revealed that all the tolerant genotypes were grouped into one sub-population, whereas the moderately tolerant and susceptible genotypes were grouped into separate sub-populations. Phylogenetic tree constructed by the unweighted neighbour-joining method also divided the genotypes into three clusters. The grouping pattern of genotypes into the clusters was similar to that into the STRUCTURE analysis, on the basis of drought tolerance level. The average value of genetic dissimilarity coefficient among the genotypes was observed to be 0.486. Furthermore, by combining genotyping data with phenotyping data, 16 new donors for 6 qDTYs were identified.

关键词： drought screening genetic relationship population structure qDTY donor upland rice grain yield

Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance

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Rice science 2016年第6期23卷 317-325页

作者： A.D.CHOWDHURY G.HARITHA T.SUNITHA S.L.KRISHNAMURTHY B.DIVYA G.PADMAVATHI T.RAM N.SARLA ICAR-Indian Institute of Rice Research Division of Crop Improvement Central Soil Salinity Research Institute

Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated withsalt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1to 9 score at EC = 10 dSm^-1 under controlled environmental conditions. Seven new breeding linesincluding three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 andcan be good sources of new genes/alleles for salt tolerance. Simple sequence repeat （SSR） markerRM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information contentvalue varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54lines were clearly separated into two major clusters. Fourteen haplotypes were identified based onSaltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminatebetween the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assistedselection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 onchromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.

关键词： haplotype rice salt tolerance Saltol simple sequence repeat marker

Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding

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The crop Journal 2017年第5期5卷 416-429页

作者： Dipnarayan Saha Rajeev Singh Rana Sukla Chakraborty Subhojit Datta Arroju Anil Kumar Asim Kumar Chakraborty Pran Gobinda Karmakar Division of Crop Improvement Indian Council of Agricultural Research (ICAR)-Central Research Institute for Jute and Allied Fibers

Corchorus capsularis(white jute) and C. olitorius(dark jute) are the two principal cultivated spedes of jute that produce natural bast fiber of commercial importance. We have identified 4509 simple sequence repeat(SSR) loci from 34,163 unigene sequences of C. capsularis to develop a non-redundant set of 2079 flanking primer pairs. Among the SSRs, trinudeotide repeats were most frequent(60%) followed by dinucleotide repeats(37.6%). Annotation of the SSR-containing unigenes revealed their putative functions in various biological and molecular processes, including responses to biotic and abiotic signals. Eighteen expressed gene-derived SSR(eSSR) markers were successfully mapped to the existing single-nucleotide polymorphism(SNP) linkage map of jute,providing additional anchor points. Amplification of 72% of the 74 randomly selected primer pairs was successful in a panel of 24 jute accessions, comprising five and twelve accessions of C.capsularis and C. olitorius, respectively, and seven wild jute spedes. Forty-three primer pairs produced an average of 2.7 alleles and 58.1% polymorphism in a panel of 24 jute accessions. The mean PIC value was 0.34 but some markers showed PIC values higher than 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci(QTLs) in jute. A primer polymorphism survey with parents of a wide-hybridized population between a cultivated jute and its wild relative revealed their efficacy for interspecific hybrid identificatioii. For ready accessibility of jute eSSR primers, we compiled all information in a user-friendly web database, JuteMarkerdb(http://jutemarkerdb.***.gov.in/) for the first time in jute.This eSSR resource in jute is expected to be of use in characterization of germplasm, interspecific hybrid and variety identification, and marker-assisted breeding of superior-quality jute.

关键词： Database Genic-SSR Jute Interspecific hybrid identification Unigene sequences

Genetic Dissection of Grain Size Traits Through Genome-Wide Association Study Based on Genic Markers in Rice

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Rice science 2022年第5期29卷 462-472,I0032-I0034页

作者： Amrit Kumar NAYAK Anilkumar C Sasmita BEHERA Rameswar Prasad SAH Gera Roopa LAVANYA Awadhesh KUMAR Lambodar BEHERA Muhammed Azharudheen TP Division of Crop Improvement Indian Council of Agricultural Research-National Rice Research InstituteCuttack 753006India division of crop Physiology and Biochemistry ICAR-National Rice Research InstituteCuttack 753006India Department of Genetics and Plant Breeding Sam Higginbottom University of AgricultureTechnology and SciencesPrayagraj 211007India

Grain size plays a significant role in rice,starting from affecting yield to consumer preference,which is the driving force for deep investigation and improvement of grain size characters.Quantitative inheritance makes these traits complex to breed on account of several alleles contributing to the complete trait expression.We employed genome-wide association study in an association panel of 88 rice genotypes using 142 new candidate gene based SSR(cgSSR)markers,derived from yield-related candidate genes,with the efficient mixed-model association coupled mixed linear model for dissecting complete genetic control of grain size traits.A total of 10 significant associations were identified for four grain size-related characters(grain weight,grain length,grain width,and length-width ratio).Among the identified associations,seven marker trait associations explain more than 10%of the phenotypic variation,indicating major putative QTLs for respective traits.The allelic variations at genes OsBC1L4,SHO1 and OsD2 showed association between 1000-grain weight and grain width,1000-grain weight and grain length,and grain width and length-width ratio,respectively.The cgSSR markers,associated with corresponding traits,can be utilized for direct allelic selection,while other significantly associated cgSSRs may be utilized for allelic accumulation in the breeding programs or grain size improvement.The new cgSSR markers associated with grain size related characters have a significant impact on practical plant breeding to increase the number of causative alleles for these traits through marker aided rice breeding programs.

关键词： best linear unbiased predictor estimate candidate gene based SSR efficient mixed-model association approach genome-wide association study VanRaden kinship

Effects of inter-culture, arabinogalactan proteins, and hydrogen peroxide on the plant regeneration of wheat immature embryos

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Journal of Integrative Agriculture 2015年第1期14卷 11-19页

作者： ZHANG Wei WANG Xin-min FAN Rong YIN Gui-xiang WANG Ke DU Li-pu XIAO Le-le YE Xing-guo National Key Facility of crop Gene Resources and Genetic improvement/Institute of crop Sciences Chinese Academy of Agricultural Sciences division of Agricultural and Environmental Science School of BiosciencesUniversity of Nottingham

The regeneration rate of wheat immature embryo varies among genotypes, howbeit many elite agriculture wheat varieties have low regeneration rates. Optimization of tissue culture conditions and attempts of adding signal molecules are effective ways to increase plant regeneration rate. Inter-culture is one of ways that have not been investigated in plant tissue culture. Moreover, the use of arabinogalactan proteins （AGPs） and hydrogen peroxide （H202） have been reported to increase regeneration rate in a few plant species other than wheat. The current research pioneeringly uses inter-culture of immature embryos of different wheat genotypes, and also investigates impacts of AGP and H2O2 on the induction of embryogenic calli and plant regeneration. As a result, high-frequency regeneration wheat cultivars Kenong 199 （KN 199） and Xinchun 9 （XC9）, together with low-frequency regeneration wheat line Chinese Spring （CS）, presented striking increase in the induction of embryogenic calli and plant regeneration rate of CS through inter-culture strategy, up to 52.19 and 67.98%, respectively. Adding 50 to 200 mg L-1 AGP or 0.005 to 0.01‰ H2O2 to the callus induction medium, enhanced growth of embryogenic calli and plant regeneration rate in quite a few wheat genotypes. At 50 mg L-1 AGP application level in callus induction medium plant regeneration rates of 8.49,409.06 and 283.16% were achieved for Jimai 22 （JM22）, Jingdong 18 （JD18） and Yangmai 18 （YM18）, respectively; whereas at 100 mg L-1 AGP level, CS （105.44%）, Chuannong 16 （CN16）（80.60%） and Ningchun 4 （NC4）（62.87%） acted the best. Moreover CS （79.05%）, JM22 （7.55%）, CN16 （101.87%）, YM18 （365.56%）, Yangmai 20 （YM20）（10.48%）, and CB301 （187.40%） were more responsive to 0.005 %o of H2O2, and NC4 （35.37%） obtained the highest shoot regeneration rates at 0.01%o of H2O2. Overall, these two methods, inter-culture and AGP （or H2O2） application, can be further applied to wheat transgenic research.

关键词： wheat immature embryos plant regeneration inter-culture arabinogalactan proteins hydrogen peroxide

Phytosterol content and the campesterol:sitosterol ratio influence cotton fiber development: role of phytosterols in cell elongation

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Science China(Life Sciences) 2016年第2期59卷 183-193页

作者： Shasha Deng Ting Wei Kunling Tan Mingyu Hu Fang Li Yunlan Zhai Shue Ye Yuehua Xiao Lei Hou Yan Pei Ming Luo Key Laboratory of Biotechnology and crop Quality improvement Ministry of AgricultureBiotechnology Research Center Southwest University

Phytosterols play an important role in plant growth and development,including cell division,cell elongation,embryogenesis,cellulose biosynthesis,and cell wall formation.Cotton fiber,which undergoes synchronous cell elongation and a large amount of cellulose synthesis,is an ideal model for the study of plant cell elongation and cell wall biogenesis.The role of phytosterols in fiber growth was investigated by treating the fibers with tridemorph,a sterol biosynthetic inhibitor.The inhibition of phytosterol biosynthesis resulted in an apparent suppression of fiber elongation in vitro or in planta.The determination of phytosterol quantity indicated that sitosterol and campesterol were the major phytosterols in cotton fibers;moreover,higher concentrations of these phytosterols were observed during the period of rapid elongation of fibers.Furthermore,the decrease and increase in campesterol:sitosterol ratio was associated with the increase and decease in speed of elongation,respectively,during the elongation stage.The increase in the ratio was associated with the transition from cell elongation to secondary cell wall synthesis.In addition,a number of phytosterol biosynthetic genes were down-regulated in the short fibers of ligon lintless-1mutant,compared to its near-isogenic wild-type TM-1.These results demonstrated that phytosterols play a crucial role in cotton fiber development,and particularly in fiber elongation.

关键词：植物甾醇细胞伸长菜油甾醇棉纤维醇含量生物合成抑制剂植物生长发育 β-谷甾醇

Dissection of heterosis for yield and related traits using populations derived from introgression lines in rice

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The crop Journal 2016年第6期4卷 468-478页

作者： Chao Xiang Hongjun Zhang Hui Wang Shaobo Wei Binying Fu Jiafa Xia Zefu Li Yongming Gao Guoyou Ye Institute of crop Sciences/National Key Facility for crop Gene Resources and Genetic improvement Chinese Academy of Agricultural Sciences Rice Research Institute Anhui Academy of Agricultural Sciences Genetics and Biotechnology division International Rice Research Institute

Despite the great success achieved by the exploitation of heterosis in rice,the genetic basis of heterosis is still not well understood.We adopted an advanced-backcross breeding strategy to dissect the genetic basis of heterosis for yield and eight related traits.Four testcross(TC) populations with 228 testcross F1 combinations were developed by crossing57 introgression lines with four types of widely used male sterile lines using a North Carolina II mating design.Analysis of variance indicated that the effects of testcross F1 combinations and their parents were significant or highly significant for most of the traits in both years,and all interaction effects with year were significant for most of the traits.Positive midparent heterosis(HMP) was observed for most traits in the four TC populations in the two years.The relative HMPlevels for most traits varied from highly negative to highly positive.Sixty-two dominant-effect QTL were identified for HMPof the nine traits in the four TC populations in the two years.Of these,22 QTL were also identified for the performance of testcross F1.Most dominant-effect QTL could individually explain more than 10% of the phenotypic variation.Four QTL clusters were observed including the region surrounding the RM9–RM297 region on chromosome 1,the RM110–RM279–RM8–RM5699–RM452 region on chromosome 2,the RM5463 locus on chromosome 6 and the RM1146–RM147 region on chromosome 10.The identified QTL for heterosis provide valuable information for dissecting the genetic basis of heterosis.

关键词： Rice Yield and related traits Introgression lines Heterosis Quantitative trait loci

Morphophysiological Diversity and Haplotype Analysis of Saltol QTL Region in Diverse Rice Landraces for Salinity Tolerance

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Rice science 2023年第4期30卷 306-320,I0010-I0012页

作者： B.M.LOKESHKUMAR S.L.KRISHNAMURTHY Suman RATHOR Arvinder Singh WARRIACH N.M.VINAYKUMAR B.M.DUSHYANTHAKUMAR Parbodh Chander SHARMA Division of Crop Improvement Central Soil Salinity Research InstituteKarnal-132001HaryanaIndia Department of Biotechnology Kuvempu UniversityShankaraghattaShimvamogga-577451KarnatakaIndia Department of Genetics and Plant Breeding University of Agricultural and Horticultural ScienceShimvamogga-577204KarnatakaIndia

Rice is sensitive to salinity stress at both the seedling and reproductive stages.The present study used 145 rice genotypes comprising of 100 landraces and 45 advanced breeding lines collected from different regions of India.These genotypes were evaluated in hydroponics under control[electrical conductivity(ECe)~1.2 dS/m]and saline(ECe~10.0 dS/m)environments along with susceptible(IR29)and tolerant(FL478)checks.The stress susceptibility index for eight morphophysiological traits was estimated.Analysis of variance showed significant differences among the genotypes for all the parameters studied in control,stress and relative stress conditions.We identified 3 landraces(Kuttimanja,Tulasimog and IET-13713I)as tolerant and 14 lines as moderately tolerant to salt stress.Strong correlations in the morphological(root and shoot lengths)and physiological traits(shoot Na^(+),Ca^(2+)and Mg^(2+)contents,and Na^(+)/K^(+)ratio)were observed under all the conditions.The hierarchical cluster analysis grouped the genotypes into five clusters,among which cluster Ⅱ comprised salt-tolerant lines.Haplotyping of Saltol region using 11 simple sequence repeat markers on 17 saline tolerant and moderately tolerant lines was conducted.Markers AP3206F,RM10793 and RM3412b,located close to SKC1 gene(11.23‒12.55 Mb),displayed diverse allelic variations and they were not related to the FL478 type.In this region,tolerant lines like Kuttimanja,IET-13713I and Tulasimog have new alleles.As a result,these lines may be suitable candidates for novel genomic regions governing rice salinity tolerance.Salt-tolerance ability of Kuttimanja,Tulasimog and IET-13713I was validated in two years in three salinity stress environments.These promising lines can be used in breeding programs to broaden the genetic base of salinity tolerance in rice,and it may help to dissect key genomic regions responsible for salinity tolerance.

关键词： haplotype salinity tolerance rice Saltol diversity SKC1 gene

The TaTCP4/10-B1 cascade regulates awn elongation in wheat(Triticum aestivum L.)

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Plant Communications 2023年第4期4卷 255-270页

作者： Wensheng Ke Jiewen Xing Zhaoyan Chen Yidi Zhao Weiya Xu Lulu Tian Jinquan Guo Xiaoming Xie Dejie Du Zihao Wang Yufeng Li Jin Xu Mingming Xin Weilong Guo Zhaorong Hu Zhenqi Su Jie Liu Huiru Peng Yingyin Yao Qixin Sun Zhongfu Ni Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and Utilization(MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Awns are important morphological markers for wheat and exert a strong physiological effect on wheat yield.The awn elongation suppressor B1 has recently been cloned through association and linkage analysis in wheat.However,the mechanism of awn inhibition centered around B1 remains to be clarified.Here,we identified an allelic variant in the coding region of B1 through analysis of re-sequencing data;this variant causes an amino acid substitution and premature termination,resulting in a long-awn phenotype.Transcriptome analysis indicated that B1 inhibited awn elongation by impeding cytokinin-and auxinpromoted cell division.Moreover,B1 directly repressed the expression of TaRAE2 and TaLks2,whose orthologs have been reported to promote awn development in rice or barley.More importantly,we found that TaTCP4 and TaTCP10 synergistically inhibited the expression of B1,and a G-to-A mutation in the B1 promoter attenuated its inhibition by TaTCP4/10.Taken together,our results reveal novel mechanisms of awn development and provide genetic resources for trait improvement in wheat.

关键词： TaTCP4/10 B1 awn length haplotype wheat