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Informative ISSR Markers Help Identify Genetically Distinct Accessions of Oryza rufipogon in Yield Improvement

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Rice science 2016年第5期23卷 225-241页

作者： G.HARITHA T.SUDHAKAR D.CHAnDRA T.RAM B.DIVYA n.sarla ICAR Indian Institute of Rice Research

Inter simple sequence repeat（ISSR） polymorphism was used to determine genetic diversity and phylogenetic relationships in 90 genotypes of wild and cultivated species of Oryza from different geographical regions of the world. In all the 17 primers used in ISSR-PCR, a total of 11 464 bands were amplified at 253 band positions/loci. The primer UBC-809 amplified the maximum bands（1 059） at 21 band positions. UBC-810 and UBC-835 amplified the minimum of 391 bands each at 7 and 14 band positions, respectively. The mean polymorphism information content ranged from 0.44 to 0.84 and resolving power ranged from 8.69 to 23.53. Un-weighted pair group method with arithmetic mean dendrogram and population structure based on the 17 primers separated all genotypes into 4 major clusters with a genetic similarity of 53%–100%. The first two clusters consisted of 30 O. rufipogon accessions each. In the third cluster, O. nivara and O. longistaminata grouped as one sub-cluster and all other O. nivara accessions and cultivars grouped as another sub-cluster. The fourth cluster had only five O. rufipogon accessions which can be a source of new genes. Four sub-populations were identified within O. rufipogon and two sub-populations within O. nivara at K = 7. A subset of six primers with high resolving power values were the most informative and grouped all genotypes almost similarly as the 17 primers did. Use of these six highly informative primers in ISSR-PCR is a cost effective and robust method for assessing genetic diversity in large germplasm collections of wild rice species.

关键词： Oryza wild species genetic diversity population structure inter simple sequence repeat

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

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 *** 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

Prediction and Expression Analysis of miRnAs Associated with Heat Stress in Oryza sativa

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Rice science 2014年第1期21卷 3-12页

作者： B.SAILAJA S.R.VOLETI D.SUBRAHMAnYAM n.sarla V.VISHnU PRASAnTH V.P.BHADAnA S.K.MAnGRAUTHIA Biotechnology Section Directorate of Rice Research Rajendranagar

Computational prediction of potential microRnAs （miRnAs） and their target genes was performed to identify the miRnAs and genes associated with temperature response in rice. The data of temperature-responsive miRnAs of Arabidopsis, and miRnAs and the whole genome data of rice were used to predict potential miRnAs in Oryza sativa involved in temperature response. A total of 55 miRnAs were common in both the species, and 27 miRnAs were predicted at the first time in rice. Target genes were searched for these 27 miRnAs in rice genome following stringent criteria. Real time PCR based on expression analysis of nine miRnAs showed that majority of the miRnAs were down regulated under heat stress for rice cultivar nagina 22. Furthermore, miR169, miR1884 and miR160 showed differential expression in root and shoot tissues of rice. Identification and expression studies of miRnAs during heat stress will advance the understanding of gene regulation under stress in rice.

关键词： miRnA Oryza sativa Arabidopsis target mRnA regulation

ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought,flood,or salinity

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2009年第2期10卷 133-141页

作者： Ch Surendhar REDDY A. Prasad BABU B.P. Mallikarjuna SWAMY K. KALADHAR n. sarla Biotechnology Laboratory Crop Improvement SectionDirectorate of Rice ResearchRajendranagar

Drought, flood, salinity, or a combination of these limits rice production. Several rice varieties are well known for their tolerance to specific abiotic stresses. We determined genetic relationship among 12 rice varieties including 9 tolerant to drought, flood, or salinity using inter-simple sequence repeat （ISSR） markers. Based on all markers, the nine tolerant varieties formed one cluster distinct from the cluster of three control varieties. The salt-tolerant varieties were closest to two flood-tolerant varieties, and together they were distinct from the drought-tolerant varieties. （GA）8YG was the most informative primer, showing the highest polymorphic information content （PIC） and resolving power （Rp）. The drought-, flood-, and salt-tolerant varieties grouped in three distinct clusters within the group of tolerant varieties, when （GA）8YG was used. Sabita was the only exception. The two aus varieties, nagina22 and FR13A, were separated and grouped with the drought- and flood-tolerant varieties, respectively, hut they were together in dendrograms based on other primers. The results show that ISSR markers associated with （GA）sYG delineated the three groups of stress-tolerant varieties from each other and can be used to identify genes/new alleles associated with the three abiotic stresses in rice germplasm.

关键词： Drought Submergence Salinity Inter-simple sequence repeat-polymerase chain reaction (ISSR-PCR) (GA)8YG nagina22 (n22) FR13A Pokkali

QTL Analysis for Grain Iron and Zinc Concentrations in Two O. nivara Derived Backcross Populations

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Rice science 2018年第4期25卷 197-207页

作者： B. P. M. SWAMY K. KALADHAR1, K. AnURADHA Anil K. BATCHU T. LOnGVAH n. sarla Indian Institute of Rice Research Rajendranagar Hyderabad 500030 India Plant Breeding Division International Rice Research Institute DAPO Box 7777 Metro Manila the Philippines International Crops Research Institute on Semi Arid Tropics Patancheru Hyderabad 502324 India national Institute of nutrition Hyderabad 500007 India

Identification of quantitative trait loci （QTLs） for grain mineral elements can assist in faster and more precise development of micronutrient dense rice varieties through marker-assisted breeding. In the present study, QTLs were mapped for Fe and Zn concentrations in two BC2F3 mapping populations derived from the crosses of O. sativa cv Swarna with two different accessions of O. nivara. In all, 10 and 8 QTLs were identified for grain Fe and Zn concentrations in population 1, and 7 and 5 QTLs were identified in population 2, respectively. Eighty percent of the QTLs detected in both populations were derived from O. nivara. Five QTLs for Fe and three QTLs for Zn explained more than 15% phenotypic variance either in interval or composite interval mapping. The locations of O. nivara derived QTLs such as qFe2.1, qFe3.1, qFe8.2 and qZn12.1 were consistently identified in both the populations. Epistatic interaction was observed only between RM106 and RM6 on chromosome 2 and between RM22 and RM7 on chromosome 3 for Fe concentration in population 1. Sixteen candidate genes for metal homeostasis were found to co-locate with 10 QTLs for Fe and Zn concentrations in both the populations. Most of the Fe and Zn QTLs were found to co-locate with QTLs for grain yield and grain quality traits. Some of the major effect QTLs identified can be used to improve rice grain Fe and Zn concentrations.

关键词： biofortification micronutrient Fe concentration Zn concentration rice wild rice quantitative trait locus gene marker assisted breeding

Molecular Mapping of QTLs for Yield and Yield-Related Traits in Oryza sativa cv Swarna × O. nivara (IRGC81848) Backcross Population

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Rice science 2011年第3期18卷 178-186页

作者： B. P. MALLIKARJUnA SWAMY K. KALADHAR M. S. RAMESHA B. C. VIRAKTAMATH n. sarla Directorate of Rice Research Rajendranagar Hyderabad India - 500030 Plant Breeding Genetics and Biotechnology Division International Rice Research Institute DAPO Box 7777 Metro Manila Philippines

Advanced backcross QTL analysis was used to identify QTLs for seven yield and yield-related traits in a BC2F2 population from the cross between a popular Oryza sativa cv Swarna and O. nivara IRGC81848. Transgressive segregants with more than 15% increased effect over Swarna were observed for all the traits except days to heading and days to 50% flowering. Thirty QTLs were detected for seven yield and yield-related traits using interval and composite interval mapping. Enhancing alleles at 13 (45%) of these QTLs were derived from O. nivara, and enhancing alleles at all the QTLs for stem diameter and rachis diameter were derived from O. nivara. Three stem diameter QTLs, two rachis diameter QTLs and one number of secondary branches QTL identified by both Interval and composite interval mapping contributed more than 15% of the total phenotypic variance. The QTL epistasis was significant for stem diameter and plot yield. The most significant QTLs qSD7.2, qSD8.1 and qSD9.1 for stem diameter, qRD9.1 for rachis diameter and qnSB1.1 for number of secondary branches are good targets to evaluate their use in marker-assisted selection. O. nivara is a good source of novel alleles for yield related traits and reveals major effect QTLs suitable for marker-assisted selection.

关键词： Oryza sativa Oryza nivara stem diameter rachis diameter yield yield components quantitative trait locus