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Screening of rice germplasm against Asian rice gall midge, Orseolia oryzae (Wood-Mason), biotypes in India has led to identification of over 300 resistant rice genotypes. However, only ten resistance genes have been characterized so far. Identification of new genes through classical allelism test is tedious and time consuming. We propose to use closely linked flanking Simple Sequence Repeat (SSR) markers in allelism tests for identification of resistance genes. Of the ten known gall midge resistance genes, eight have been tagged and mapped. The Gm1 and Gm2 genes have closely linked flanking markers. Hence SSR markers RM219 and RM444, flanking the gene Gm1, and RM317, RM241 along with the SCAR marker F8, flanking the gene Gm2, were selected for this study. Tests with one set of 13 genotypes likely to carry Gm1 and another set of 17 genotypes suspected to contain Gm2 suggested the presence of the respective allele in all the 13 and 15 genotypes from these sets, respectively. Classical allelism test perfectly matched with the markers test. There were two exceptions involving amplification with RM444 in cultivar Kavya and with RM241 in genotype AE20, suggesting a single recombination which could have resulted in the mismatch. All the three markers in the genotype Bhumansan and the two flanking markers RM317 and F8 in AE20 indicated the absence of the Gm2 allele. This was validated through a classical test, revealing a segregation ratio of 15 resistant: 1 susceptible F2 progeny of both the crosses between the Gm2 source Phalguna and these genotypes. We performed the allelism test with the markers on another set of 56 randomly selected gall midge resistant genotypes to discover possible sources of new resistance genes. 相似文献
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Basvaraj C. Viraktamath Arremsetty S. Hariprasad Gouri S. Laha Mohammed I. Ahmed Podishetty Natarajkumar Mugalodi S. Ramesha Chirravuri N. Neeraja Sena M. Balachandran Nallathigal S. Rani Pippalla Balaji Suresh Kalidindi Sujatha Manish Pandey Gajjala Ashok Reddy Maganti S. Madhav Raman M. Sundaram 《Plant Breeding》2011,130(6):608-616
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Passoupathy Rajendrakumar Akshaya Kumar Biswal Kannabiran Sakthivel Maganti Sheshu Madhav Chirravuri Neeraja Sena M. Balachandran Kommoju Srinivasarao Podishetty Natarajkumar Yadla Hari Kalidindi Sujatha Raman M. Sundaram 《Euphytica》2009,169(2):263-271
SSR markers targeting (GATA)
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motifs are known to be highly polymorphic and useful in many organisms. (GATA)
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motif specific SSR markers covering the whole rice genome are not available. The present study was carried out with an objective
to identify class I rice microsatellites in the rice genome with (GATA)n motifs, in-silico, and validate their potential as molecular markers. A total of 243 such motifs were identified; 65 of these
were present in the genic region, 59 were in the upstream region and the remaining motifs were found in the intergenic regions.
Many of the (GATA)
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motifs were found within and/or upstream of genes associated with biotic or abiotic stress tolerance. A total of 230 PCR-based
markers targeting all the class I (GATA)
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microsatellites were developed and 35 of these markers spread across the rice genome were validated in a set of 24 representative
rice varieties belonging to five distinct cultivar groups. All the markers were polymorphic, with average polymorphism information
content (PIC) value of 0.61, and the rice cultivars could be uniquely distinguished into different cultivar groups based on
marker analysis. These informative markers targeting (GATA)
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motifs representing a new set of markers in rice will be highly useful for genetic studies and marker-assisted selection.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Passoupathy Rajendrakumar, Akshaya Kumar Biswal and Kannabiran Sakthivel contributed equally. 相似文献
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P. Balaji Suresh B. Srikanth V. Hemanth Kishore I. Subhakara Rao L. R. Vemireddy N. Dharika R. M. Sundaram M. S. Ramesha K. R. S. Sambasiva Rao B. C. Viraktamath C. N. Neeraja 《Euphytica》2012,187(3):421-435
The Wild Abortive (WA) system is the major cytoplasmic male sterility (CMS) source for hybrid rice production in indica rice and its fertility restoration is reported to be controlled by two major loci viz. Rf3 on chromosome 1 and Rf4 on chromosome 10. With the availability of the rice genome sequence, an attempt was made to fine map, develop candidate gene based markers for Rf3 and Rf4 and validate the developed marker system in a set of known restorer lines. Using polymorphic markers developed from microsatellite markers and candidate gene based markers from Rf3 and Rf4 loci, local linkage maps were constructed in two mapping populations of ~1,500 F2 progeny from KRH2 (IR58025A/KMR3R) and DRRH2 (IR68897A/DR714-1-2R) hybrids. QTLs and their interactions for fertility restoration in Rf3 and Rf4 loci were identified. The identified QTL in both mapping populations together explained 66–72 % of the phenotypic variance of the trait suggesting their utility in developing a marker system for identification of fertility restorers for WA-CMS. Sequence comparison of the two candidate genes from the Rf3 and Rf4 regions in male sterile (A) and restorer (R) lines showed 2–3 bp indels and a few substitutions in the Rf3 region and indels of 327 and 106 bp in the Rf4 region respectively. The marker system identified in the present study was validated in 212 restorers and 34 maintainers along with earlier reported markers for fertility restoration of WA-CMS. Together DRCG-RF4-14 and DRCG-RF4-8 for the Rf4 locus and DRRM-RF3-5/DRRM-RF3-10 for the Rf3 locus showed a maximum efficiency of 92 % for identification of restorers. 相似文献
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Yields in the irrigated rice areas have improved remarkably over the last three decades. Farmers with access to assured water supply have adopted improved varieties resulting in higher yields improved income in rural areas.…… 《分子植物育种》2007,5(2):207-208
Yields in the irrigated rice areas have improved remarkably over the last three decades. Farmers with access to assured water supply have adopted improved varieties, resulting in higher yields and improved income in rural areas. In contrast, yields remain low in the vast rainfed areas that are associated with higher levels of poverty. A few improved varieties have spread in these areas, but abiotic stresses such as drought and submergence prevent farmers from realizing their yield potential. Stress tolerant versions of these varieties are urgently needed to improve the standard of living and stabilize household food supplies. It has been found that tolerance to a number of abiotic stresses is controlled by a few QTLs of large effect, and that incorporation of these QTLs into the high yielding varieties could make a significant impact in stabilizing the yields of these varieties in stress-prone areas （Mackiil, 2006）. Submergence tolerance provides a good example of how marker assisted selection can be very effective to develop improved varieties for the rainfed lowlands. 相似文献
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Kumar PN Sujatha K Laha GS Rao KS Mishra B Viraktamath BC Hari Y Reddy CS Balachandran SM Ram T Madhav MS Rani NS Neeraja CN Reddy GA Shaik H Sundaram RM 《Phytopathology》2012,102(2):222-228
Broadening of the genetic base for identification and transfer of genes for resistance to insect pests and diseases from wild relatives of rice is an important strategy in resistance breeding programs across the world. An accession of Oryza nivara, International Rice Germplasm Collection (IRGC) accession number 105710, was identified to exhibit high level and broad-spectrum resistance to Xanthomonas oryzae pv. oryzae. In order to study the genetics of resistance and to tag and map the resistance gene or genes present in IRGC 105710, it was crossed with the bacterial blight (BB)-susceptible varieties 'TN1' and 'Samba Mahsuri' (SM) and then backcrossed to generate backcross mapping populations. Analysis of these populations and their progeny testing revealed that a single dominant gene controls resistance in IRGC 105710. The BC(1)F(2) population derived from the cross IRGC 105710/TN1//TN1 was screened with a set of 72 polymorphic simple-sequence repeat (SSR) markers distributed across the rice genome and the resistance gene was coarse mapped on chromosome 7 between the SSR markers RM5711 and RM6728 at a genetic distance of 17.0 and 19.3 centimorgans (cM), respectively. After analysis involving 49 SSR markers located between the genomic interval spanned by RM5711 and RM6728, and BC(2)F(2) population consisting of 2,011 individuals derived from the cross IRGC 105710/TN1//TN1, the gene was fine mapped between two SSR markers (RMWR7.1 and RMWR7.6) located at a genetic distance of 0.9 and 1.2 cM, respectively, from the gene and flanking it. The linkage distances were validated in a BC(1)F(2) mapping population derived from the cross IRGC 105710/SM//2 × SM. The BB resistance gene present in the O. nivara accession was identified to be novel based on its unique map location on chromosome 7 and wider spectrum of BB resistance; this gene has been named Xa33. The genomic region between the two closely flanking SSR markers was in silico analyzed for putatively expressed candidate genes. In total, eight genes were identified in the region and a putative gene encoding serinethreonine kinase appears to be a candidate for the Xa33 gene. 相似文献
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I. Jaikishan P. Rajendrakumar M. S. Ramesha B. C. Viraktamath S. M. Balachandran C. N. Neeraja K. Sujatha K. Srinivasa Rao P. Natarajkumar Y. Hari K. Sakthivel A. S. Ramaprasad R. M. Sundaram 《Plant Breeding》2010,129(1):108-111
This study was undertaken to assess the comparative potential of 25 Expressed Sequence Tag derived simple sequence repeats (EST-SSRs) and 25 genomic SSRs in the prediction of grain yield heterosis using a set of nine cytoplasmic male sterile (CMS) lines and 32 restorer lines of rice. EST-SSRs and genomic SSRs exhibited an average Polymorphism Information Content value of 0.37 and 0.45, respectively. The coefficient of marker polymorphism among parental lines with respect to a set of hypervariable EST and genomic SSRs was correlated with standard heterosis for grain yield of six public bred rice hybrids. EST-SSRs gave a better correlation (r = 0.75) as compared with genomic SSRs (r = 0.09). When 10 'key' informative EST-SSR markers which showed a higher positive correlation with grain yield heterosis were validated in a new set of 14 experimental hybrids, the markers exhibited a higher correlation (r = 0.79), indicating the predictive value of these EST-SSRs. We recommend these 10 'key' informative EST-SSR markers for analysis of genetic diversity of parental lines and prediction of heterosis in hybrid rice breeding programmes. 相似文献
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Kommoju Srinivasarao Basavaraj C. Viraktamath Arremsetty S. Hari Prasad Gouri S. Laha Mohammed I. Ahmed Podishetty Natarajkumar Kalidindi Sujatha Madamshetty Srinivas Prasad Manish Pandey Mugalodi S. Ramesha Chirravuri N. Neeraja Sena M. Balachandran Nallathigal S. Rani Balachandra Kemparaju Kolluru Madhan Mohan Venkata S. A. K. Sama Hajira Shaik Chintavaram Balachiranjeevi Karnati Pranathi Gajjala Ashok Reddy Maganti S. Madhav Raman M. Sundaram 《Plant Breeding》2013,132(6):586-594
IR 58025A is a very popular wild‐abortive cytoplasmic male sterile (WA‐CMS) line of rice and is extensively used for hybrid rice breeding. However, IR 58025A and many hybrids derived from it possess mild aroma (undesirable in some parts of India) and are highly susceptible to bacterial blight (BB) and blast diseases. To improve IR 58025A for BB and blast resistance, we have introgressed a major dominant gene conferring resistance against BB (i.e. Xa21) and blast (i.e. Pi54) into IR 58025B, the maintainer line of IR 58025A. An introgression line of Samba Mahsuri (i.e. SM2154) possessing Xa21 and Pi54 genes in homozygous condition and fine‐grain type was used as donor parent, and backcross breeding strategy was adopted for targeted introgression of the resistance genes. PCR‐based molecular markers tightly linked to Xa21 and Pi54 were used for selection of BB‐ and blast‐resistant lines, while closely linked markers were used for identification of backcross‐derived plants devoid of Rf4 and aroma. At BC2F5, four backcross‐derived lines possessing resistance against BB and blast, devoid of aroma, high yield, short plant stature, long‐slender grain type and with recurrent parent genome recovery ranging from 88.8% to 98.6% were selected and advanced for further evaluation. The improved versions of IR 58025B, viz. SB54‐11‐143‐9‐44‐5, SB54‐11‐143‐9‐44‐98, SB54‐11‐143‐9‐44‐111 and SB54‐11‐143‐9‐44‐171, behaved as perfect maintainers when test‐crossed with WA‐CMS lines. Agronomically superior lines of improved IR 58025B are being converted to CMS line through backcrossing for developing high‐yielding and biotic stress‐resistant rice hybrids. 相似文献
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