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

Plant Breeding (Impact Factor: 1.6). 04/2008; 127(2):131—139. DOI: 10.1111/j.1439-0523.2007.01458.x


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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Available from: Anand Kullan, Feb 15, 2014
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    • "Further, the phenotypic selection among the plants with maximum RPG recovery, hastened the recovery of RPP. The efficacy of background selection combined with phenotypic selection in recovering RPP in rice has been demonstrated earlier (Joseph et al. 2004; Gopalakrishnan et al. 2008; Singh et al. 2011, 2012, 2013). "
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    ABSTRACT: Key message: A set of NILs carrying major blast resistance genes in a Basmati rice variety has been developed. Also, the efficacy of pyramids over monogenic NILs against rice blast pathogen Magnaporthe oryzae has been demonstrated. Productivity and quality of Basmati rice is severely affected by rice blast disease. Major genes and QTLs conferring resistance to blast have been reported only in non-Basmati rice germplasm. Here, we report incorporation of seven blast resistance genes from the donor lines DHMASQ164-2a (Pi54, Pi1, Pita), IRBLz5-CA (Pi2), IRBLb-B (Pib), IRBL5-M (Pi5) and IRBL9-W (Pi9) into the genetic background of an elite Basmati rice variety Pusa Basmati 1 (PB1). A total of 36 near-isogenic lines (NILs) comprising of 14 monogenic, 16 two-gene pyramids and six three-gene pyramids were developed through marker-assisted backcross breeding (MABB). Foreground, recombinant and background selection was used to identify the plants with target gene(s), minimize the linkage drag and increase the recurrent parent genome (RPG) recovery (93.5-98.6 %), respectively, in the NILs. Comparative analysis performed using 50,051 SNPs and 500 SSR markers revealed that the SNPs provided better insight into the RPG recovery. Most of the monogenic NILs showed comparable performance in yield and quality, concomitantly, Pusa1637-18-7-6-20 (Pi9), was significantly superior in yield and stable across four different environments as compared to recurrent parent (RP) PB1. Further, among the pyramids, Pusa1930-12-6 (Pi2+Pi5) showed significantly higher yield and Pusa1633-7-8-53-6-8 (Pi54+Pi1+Pita) was superior in cooking quality as compared to RP PB1. The NILs carrying gene Pi9 were found to be the most effective against the concoction of virulent races predominant in the hotspot locations for blast disease. Conversely, when analyzed under artificial inoculation, three-gene pyramids expressed enhanced resistance as compared to the two-gene and monogenic NILs.
    Theoretical and Applied Genetics 04/2015; 128(7). DOI:10.1007/s00122-015-2502-4 · 3.79 Impact Factor
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    • "Hence, we resorted to phenotype-based visual selection for long-slender grain type, starting from BC 1 F 1 generation onwards, and due to a stringent selection involving screening a large number of backcross plants, we were successful in identifying the plants that not only possessed blast and BB resistance but also long-slender grain type. Earlier, Joseph et al. (2004), Gopalakrishnan et al. (2008), Sundaram et al. (2008) and Hari et al. (2011) adopted a strategy of morphology-based selection for grain type coupled with marker-based selection of target trait (i.e. bacterial blight resistance) while developing improved versions of Pusa Basmati-1, Samba Mahsuri and KMR-3R. "
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    ABSTRACT: AbstractIR 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.
    Plant Breeding 12/2013; 132(6). DOI:10.1111/pbr.12056 · 1.60 Impact Factor
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    • "Population structure analysis revealed that a set of 11 genotypes from four rice sub-populations (Tripura Medicinal Rice, five improved high-yielding long-grained Basmati and five upland indica/possibly aus type) had population admixture (>16%) with more than one genetic background, which may have resulted from their complex breeding history involving intercrossing and introgression between germplasm coupled with strong selection pressure. This was evident from clustering of five improved high-yielding long-grained Basmati within the indica sub-population in our study, which is expected because all improved Basmati genotypes were developed through cross-breeding involving non-aromatic indica and traditional Basmati germplasm [62,63]. The five indica types such as Nagina22 that showed about 15% admixture with O. rufipogon were predicted as aus type [40,64] under this category [65]. "
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    ABSTRACT: Background Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. Results Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. Conclusions SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice.
    BMC Genomics 08/2012; 13(1):426. DOI:10.1186/1471-2164-13-426 · 3.99 Impact Factor
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