Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice

Plant Breeding (Impact Factor: 1.34). 04/2008; 127:131—139. DOI: 10.1111/j.1439-0523.2007.01458.x

ABSTRACT Basmati rice is highly susceptible to bacterial blight (BB) caused by
Xanthomonas oryzae pv. oryzae. Transfer of BB resistance genes from
non-Basmati sources to Basmati through cross-hybridization requires
strict monitoring for recovery of the desirable Basmati quality traits in
the recombinants, which show complex inheritance pattern. We
integrated background analysis using mapped microsatellite markers
with foreground selection to identify superior lines that combine useful
genes from a non-Basmati BB resistance donor line IRBB55 with grain
and cooking quality characteristics of the popular Basmati rice variety
Pusa Basmati 1(PB 1) employing backcross pedigree strategy.
Foreground selection using linked markers ensured presence of two
genes, xa13 and Xa21 for BB resistance from IRBB55, and the
recurrent parent PB 1 allele for the waxy locus giving intermediate
amylose content and maintainer allele at fertility restorer locus in the
BC1F5 recombinants. Background analysis enabled selection of
recombinants with recurrent parent genome to the extent of 86.3%
along with the quality traits. The extent of introgression of non-
Basmati donor chromosome segments in the superior selections was
estimated to be <7.8 Mb and <6.7 Mb in the xa13 and Xa21 linked
genomic regions, respectively. Association mapping identified three
quantitative trait loci, one each for 1000-grain weight, fertile grains/
panicle and cooked kernel length. The backcross-pedigree breeding
strategy facilitated recovery of additional desirable characteristics from
the donor in some of the selections. The elite selection Pusa 1460-01-
32-6-7-67 with maximum genomic background and quality characteristics
of the recurrent Basmati parent gave resistance reaction against
BB, similar to that of the non-Basmati resistant check variety and
recorded an yield advantage of 11.9% over the best check in the
multiplication agronomic trial in the Basmati growing region of India.
This line, which has been released as a new variety in the name of
Improved Pusa Basmati 1 for commercial cultivation in India, is an
example of successful application of marker assisted selection to
variety development.

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    ABSTRACT: Marker‐assisted simultaneous but stepwise backcross breeding (MASS‐BB) was utilized in the present study for pyramiding blast resistance genes, Piz5 and Pi54, from non‐Basmati donors, C101A51 and Tetep, respectively, into PRR78, an elite Basmati restorer line of rice hybrid, Pusa RH10. Marker‐assisted foreground selection coupled with stringent phenotypic selection and background analysis was carried out for hastening the recovery of recurrent parent phenome (RPP) and genome (RPG) in two separate backcross series to produce BC2F1 plants with individual blast resistance gene. The best BC2F1 plant from each backcross series was intercrossed, and the resultant F1 was selfed to pyramid both blast‐resistance genes into PRR78. The plants homozygous for both the genes in the F2 were advanced through pedigree selection to produce superior blast‐resistant F5 lines. Background analysis revealed that the RPG recovery was up to 91.6%. Improved versions of Pusa RH10 developed using the improved PRR78 lines (PRR78+Piz5+Pi54) performed on par with the original Pusa RH10 and showed resistance to blast disease both under artificial screening and at hot spot locations.
    Plant Breeding 06/2013; 132(5). · 1.34 Impact Factor
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    ABSTRACT: Development and large-scale genotyping of single-nucleotide polymorphism (SNP) is required to use identified sequence variation in the alleles of different genes to determine their functional relevance to the candidate gene(s). In the present study, Illumina GoldenGate assay was used to validate and genotype SNPs in a set of six major rice blast resistance genes, viz. Pi-ta, Piz(t), Pi54, Pi9, Pi5(1) and Pib, distributed over five chromosomes, to understand their functional relevance and study the population structure in rice. All the selected SNPs loci (96) of six blast (Magna-porthe oryzae) resistance genes were genotyped successfully in 92 rice lines with an overall genotype call rate of 92.0 % and minimum GenTrain cutoff score of C0.448. The highest genotyped SNPs were found in japonica type (97.1 %) rice lines, followed by indica (92.12 %), indica basmati (91.84 %) and minimum in case of wild species (82.0 %). Among the genotyped loci, the highest score (98.68 %) was observed in case of Piz(t), followed by Pi-ta, Pi5(1), Pib, Pi54 and Pi9. Polymorphism was obtained in 87.5 % SNPs loci producing 7,728 genotype calls. Minor allele frequency ranged from 0.01 to 0.49 and Electronic supplementary material The online version of this article (doi:10.1007/s11032-014-0129-9) contains supple-mentary material, which is available to authorized users.
    Molecular Breeding 06/2014; · 2.28 Impact Factor
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    ABSTRACT: Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae and blast caused by Magnaporthe oryzae are major constraints that limit rice productivity. Marker-assisted backcross breeding was used to incorporate BB resistance genes (xa13 and Xa21) and blast resistance genes (Piz5 and Pi54) into the genetic background of an elite basmati restorer line, PRR78, which resulted in the development of Pusa1601 (PRR78 + xa13 + Xa21) and Pusa 1609 (PRR78 + Piz5 + Pi54), respectively. Furthermore, in order to combine the genes xa13, Xa21, Piz5, and Pi54 into the genetic background of PRR78, Pusa 1601 and Pusa 1609 were intercrossed to develop Pusa 1790, and foreground marker-verifed true F1 plants were selfed to generate an F2 population of 1,509 individuals. Stringent phenotypic selection was used to identify 400 plants resembling PRR78, which underwent foreground analysis. A total of three, fve and 16 plants homozygous for four, three and two genes in different combinations, respectively, were identifed and advanced to F3. In F3, evaluation for agronomic performance, disease reactions under artifcial inoculations, and grain and cooking quality traits was performed, leading to the development of improved lines of PRR78. These lines, designated with the prefx Pusa 1790, carry genes xa13 + Xa21 for BB resistance and Piz5 + Pi54 for blast resistance. Hybrids using improved restorer lines have been generated to evaluate their heterotic potential.
    Public-private partnership for hybrid rice. Proceedings of the 6th International Hybrid Rice Symposium, Edited by Xie F, Hardy B, 01/2014: pages 261-272; International Rice Research Institute., ISBN: 978-971-22-0303-9


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