Browsing by Author "Sinha, Pallavi"

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    Genomics-assisted breeding for boosting crop improvement in pigeon pea (Cajanus cajan)
    (Frontiers in plant science, 2015) Pazhamala, Lekha; Saxena, Rachit K.; Singh, Vikas K.; Sameerkumar, C.V.; Kumar, Vinay; Sinha, Pallavi; Patel, Kishan; Obala, Jimmy; R.Kaoneka, Seleman; Tongoona, P.; Shimelis, Hussein A.; Gangarao, N.V.P.R.; Odeny, Damaris; Rathore, Abhishek; Dharmaraj, P.S.; Yamini, K. N.; Varshney, Rajeev K.
    Pigeon pea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeon pea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeon pea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeon pea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeon pea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeon pea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeon pea breeding.
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    QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea
    (Heredity, 2022) Singh, Vikas; Sinha, Pallavi; Obala, Jimmy; Khan, Aamir W.; Chitikineni, Annapurna; Saxena, Rachit K.; Varshney, Rajeev K.
    To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and lateflowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTLseq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement.