[show abstract][hide abstract] ABSTRACT: 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 testcrossed
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.
[show abstract][hide abstract] ABSTRACT: 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.
[show abstract][hide abstract] ABSTRACT: The cultivar Ajaya (IET 8585) exhibits durable broad-spectrum resistance to bacterial blight (BB) disease of rice and is widely used as a resistance donor. The present study was carried out to decipher the genetics of BB resistance in Ajaya and map the gene(s) conferring resistance. Genetic analysis in the F2 indicated a quantitative/additive nature of resistance governed by two loci with equal effects. Linked marker analysis and allelic tests revealed that one of the resistance genes is xa5. Sequence analysis of a 244 bp region of the second exon of the gene-encoding Transcription factor IIAγ (the candidate gene for xa5) confirmed the presence of xa5. Bulked-segregant analysis (BSA) revealed the putative location of the two quantitative trait loci (QTLs)/genes associated with resistance on chromosomes 5 and 8. Composite interval mapping located the first locus on Chr. 5S exactly in the genomic region spanned by xa5 and the second locus (qtl BBR 8.1) on Chr. 8L. Owing to its differential disease reaction with a set of seven hyper-virulent isolates of Xanthomonas oryzae, a map location on Chr. 8L, which was distinct from xa13 and data from allelism tests, the second resistance locus in Ajaya was determined to be novel and was designated as xaAj. A contig map spanning xaAj was constructed in silico and the genomic region was delimited to a 13.5 kb physical interval. In silico analysis of the genomic region spanning xaAj identified four putatively expressed candidate genes, one of which could be involved in imparting BB resistance in Ajaya along with xa5.
Genetics Research 12/2011; 93(6):397-408. · 2.00 Impact Factor
[show abstract][hide abstract] ABSTRACT: With 2 tablesAbstractThis 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.
[show abstract][hide abstract] ABSTRACT: SSR markers targeting (GATA)
motifs are known to be highly polymorphic and useful in many organisms. (GATA)
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)
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)
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)
motifs representing a new set of markers in rice will be highly useful for genetic studies and marker-assisted selection.