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.
    Full-text · Article · Apr 2015 · Theoretical and Applied Genetics
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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.
    Full-text · Article · Dec 2013 · Plant Breeding
    • "These results indicated that rice lines with higher number of Xa genes tend to display higher levels and/or wider spectra of resistance to BB than rice lines with single Xa gene. Evidences suggested that the gene interaction or quantitative complementation between the resistance genes might play the key role in increasing the level of resistance against broader spectrum of Xoo strains (Yoshimura et al., 1995;Huang et al., 1997;Gopalakrishnan et al., 2008). Our results showed that xa5 was more effective against Thai Xoo strains while Xa21 was more effective against Myanmar Xoo strains. "
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    ABSTRACT: tBacterial blight disease (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat to riceyield in rainfed and irrigated lowland ecosystems in Myanmar. Large-scale and long-term cultivation ofreleased Myanmar rice varieties have continuously caused the outbreak of BB since 1983. In this study, ahigh yielding Manawthukha rice line ‘Yn 3248-2-128-76-4-3-75’ (MK-75) with fragrance and intermedi-ate amylose content was used as a recipient parent to improve its resistance to BB. RGDU-07097-1-8M-9(RG-9), an improved line carrying xa5, Xa21 and xa33 was used as the donor parent. Resistant alleles ofxa5, Xa21 and xa33 from RG-9 were successfully transferred into MK-75 by using marker-assisted back-crossing (MAB) method while maintaining the cooking quality of MK-75. Twenty eight selected BC3F2introgression lines (MK-75 ILs) carrying different combinations of these three loci were tested for BBresistance at seedling and maximum tillering stages against ten Thai and five Myanmar Xoo strains. Thetriple and double resistance gene-introgressed lines (xa5Xa21xa33 or xa5Xa21 or xa5xa33 or Xa21xa33)had higher level of resistance and wider resistance spectrum than MK-75 against both Thai and MyanmarXoo strains. The single resistance gene-introgressed lines carrying xa5 had higher resistance against ThaiXoo strains, while lines carrying Xa21 showed higher level of resistance to Myanmar Xoo strains. Theseresults clearly indicated that pyramiding of multiple genes is a useful approach for improving BB resis-tance in MK-75. All ILs had physical grain quality, fragrance and amylose content similar to MK-75. Thusthe improvement of BB resistance in MK-75 may have a wide range of benefits in breeding program andshould be immediately useful in areas where original Manawthukha, the progenitor or MK-75 is widelygrown.
    No preview · Article · Aug 2013 · Field Crops Research
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