Pusa Basmati 1121 – a rice variety with exceptional kernel elongation and volume expansion after cooking

Daware

et al. 2019

Preprint

Rice grain size and weight are major determinant of grain quality and yield and so have been under rigorous selection since domestication. However, genetic basis for contrasting grain size/weight trait among indian germplasm, and their association with domestication shaped evolutionary region is not studied before. To identify genetic basis of grain size/weight two long (LGG) and two short grain genotypes (SGG) were resequenced. LGG (LGR and Pusa Basmati 1121) differentiated from SGG (Sonasal and Bindli) by 504439SNPs and 78166 InDels. The LRK gene cluster was significantly affected and a truncation mutation in the LRK8 kinase domain was uniquely associated with LGG. Phylogeny with 3000 diverse rice accessions revealed four sequenced genotypes belonged to japonica group and were at the edge of clades indicating source of genetic diversity available in Asian rice population. Five SNPs significantly were associated with grain size/weight and top three SNPs were validated in RIL mapping populations, suggesting this study as a valuable resource for high-throughput genotyping. A contiguous ~6 Mb polymorphism desert region carrying a major grain weight QTL was identified on chromosome 5 in four sequenced genotypes. Further, among 3000, this region was identified as evolutionary important site with significant positive selection, elevated LD, and multiple selection sweeps, stabilising many domestication-related traits including grain size/weight. The aus group genotype retained more allelic variations in the desert region than japonica and indica, and likely to be one of the differentiation point for aus group. We suggest this desert region as an important evolutionary node that can be selected in breeding programs for improvement of grain yield and quality. All data and analysis can be accessed from RiceSzWtBase database. Significance statementBeing an important trait, rice grain size/weight has been under rigorous selection since domestication.However, a link between this trait and domestication is not so directly established. In addition to characterization of novel grain size/weight-associated SNPs, in this study, ~ 6 Mb polymorphism desert region harboring major grain weight QTL was identified on chromosome 5, which turned out to be an evolutionary important site with multiple selection sweeps and introgression events, significantly correlated with domestication-related traits.

Section: Phylogeny Estimation Of Four Sequenced Genotypessupporting

confidence: 90%

Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL

Daware

et al. 2019

Preprint

“…PB 1121, developed by our group at ICAR-Indian Agricultural Research Institute (IARI), New Delhi, is a Basmati rice variety par excellence in grain and cooking quality with an exceptionally high cooked kernel length (22 mm) and elongation ratio of > 2.5. This variety is currently grown on approximately 1.2 million ha area (60% of the Basmati area in India) and contributes annually 3.41 billion USD to foreign exchange earnings through the export of Basmati rice (Singh et al 2018b).…”

Section: Plant Materialsmentioning

confidence: 99%

Marker Assisted Development and Characterization of Herbicide Tolerant Near Isogenic Lines of a Mega Basmati Rice Variety, “Pusa Basmati 1121”

Grover

Yadav

et al. 2020

Rice

Self Cite

Background Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. Results We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) “Robin” into the genetic background of an elite popular Basmati rice variety, Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC4F4 near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin. Conclusion Overall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety, PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.

“…Development of Improved Pusa Basmati 1 involved transfer of two genes for bacterial blight resistance (xa13, Xa21) from a non-Basmati source, IRBB55 into a popular semi-dwarf, high yielding Basmati rice variety, Pusa Basmati 1 (Joseph et al 2004). Basmati rice is uniquely known for its grain and cooking quality (Singh et al 2018b), due to which there is a potential risk of impairing the grain and cooking quality especially when non-Basmati rice genotypes were used as donors for gene(s)/QTLs governing the target traits. In our programme, to recover the Basmati traits we have incorporated phenotypic selection focussing on grain and cooking quality recovery.…”

Section: Factors That Enabled Successful Integration Of Mas In Rice Bmentioning

confidence: 99%

“…Classical pedigree breeding based Basmati rice research at ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi spanning over two decades led to development of world's first semi-dwarf high yielding Basmati rice cultivar released for cultivation in 1989 (Singh and Krishnan, 2016). The release of Pusa Basmati 1121 was another milestone in terms of improving cooked kernel elongation in Basmati rice (Singh et al 2018b) which was followed by release of Pusa Basmati 6. The release of a climate smart Basmati rice variety, Pusa Basmati 1509 improved the net returns of farmers due to its short duration (120 days) and higher [Vol.…”

Section: Introductionmentioning

confidence: 99%

Precision breeding with genomic tools: A decade long journey of molecular breeding in rice

Singh¹,

Krishnan²,

Vinod³

et al. 2019

IJGPB

Plant breeding helps in recombining and fixation of desirable alleles which enables the development of improved varieties with better productivity. Though classical plant breeding has contributed enormously in achieving genetic gains in different crops including rice, the challenges imposed by resource constraints as well as greater anticipated demand need better tools to meet the expectations. Molecular breeding which uses modern genomic tools integrated with plant breeding offers enormous potential for improvement of crop varieties. The present review focusses on the achievements of ICAR-IARI in molecular breeding in rice wherein as many as eight rice varieties were incorporated with genes governing resistance/tolerance to different traits and released for commercial cultivation in India. The various factors which enabled the successful integration of molecular breeding including development of infrastructure, human resources and the genetic and genomic resources have been discussed in detail. All the examples of translational research are from the marker assisted backcross breeding strategy, which limits the scope for achieving yield gains. In the foregoing discussion, the challenges and the opportunities for implementation of molecular breeding in rice to realize the full potential of these tools in plant breeding are discussed based on the decade long experience, which may be valuable for other crops as well.