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An improved draft of the pigeonpea (Cajanus cajan (L.) Millsp.) genome.

ABSTRACT: The first draft of the pigeonpea (Cajanus cajan (L.) Millsp. cv. Asha) genome with 511 Mbp of assembled sequence information has low genome coverage of about sixty percent. Here we present an improved version of this genome with 648.2 Mbp of assembled sequence of this popular pigeonpea variety, which is liked by the millers and has resistance to fusarium wilt and sterility mosaic diseases. With the addition of 137 Mb of assembled sequence information the present version has the highest available genome coverage of pigeonpea till date. We predicted 56,888 protein-coding genes of which 54,286 (96.7%) were functionally annotated. In the improved genome assembly we identified 158,432 SSR loci, designed flanking primers for 85,296 of these and validated them in-silico by e-PCR. The raw data used for the improvement of genome assembly are available in the SRA database of NCBI with accession numbers SRR5922904, SRR5922905, SRR5922906, SRR5922907. The genome sequence update has been deposited at DDBJ/EMBL/GenBank under the accession AFSP00000000, and the version described in this paper is the second version (AFSP02000000).

SUBMITTER: Mahato AK

PROVIDER: S-EPMC5723258 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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An improved draft of the pigeonpea (<i>Cajanus cajan</i> (L.) Millsp.) genome.

Mahato Ajay Kumar AK Sharma Ajay Kumar AK Sharma Tilak Raj TR Singh Nagendra Kumar NK

Data in brief 20171122

The first draft of the pigeonpea (<i>Cajanus cajan</i> (L.) Millsp. cv. Asha) genome with 511 Mbp of assembled sequence information has low genome coverage of about sixty percent. Here we present an improved version of this genome with 648.2 Mbp of assembled sequence of this popular pigeonpea variety, which is liked by the millers and has resistance to fusarium wilt and sterility mosaic diseases. With the addition of 137 Mb of assembled sequence information the present version has the highest av ...[more]

PMID: 29234695

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Project description:Genome assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in next generation sequencing. Of late several draft assemblies have been reported in sequenced plant genomes. The reported draft genome assemblies of Cajanus cajan have different levels of genome completeness, a large number of repeats, gaps, and segmental duplications. Draft assemblies with portions of genome missing are shorter than the referenced original genome. These assemblies come with low map accuracy affecting further functional annotation and the prediction of gene components as desired by crop researchers. Genome coverage, i.e., the number of sequenced raw reads mapped onto a certain location of the genome is an important quality indicator of completeness and assembly quality in draft assemblies. The present work aimed to improve the coverage in reported de novo sequenced draft genomes (GCA_000340665.1 and GCA_000230855.2) of pigeonpea, a legume widely cultivated in India. The two recently sequenced assemblies, A1 and A2 comprised 72% and 75% of the estimated coverage of the genome, respectively. We employed an assembly reconciliation approach to compare the draft assemblies and merge them, filling the gaps by employing an algorithm size sorting mate-pair library to generate a high quality and near complete assembly with enhanced contiguity. The majority of gaps present within scaffolds were filled with right-sized mate-pair reads. The improved assembly reduced the number of gaps than those reported in draft assemblies resulting in an improved genome coverage of 82.4%. Map accuracy of the improved assembly was evaluated using various quality metrics and for the presence of specific trait-related functional genes. Employed pair-end and mate-pair local libraries helped us to reduce gaps, repeats, and other sequence errors resulting in lengthier scaffolds compared to the two draft assemblies. We reported the prediction of putative host resistance genes against Fusarium wilt disease by their performance and evaluated them both in wet laboratory and field phenotypic conditions.

Project description:BackgroundPigeonpea is an important grain legume of the semi-arid tropics and sub-tropical regions where it plays a crucial role in the food and nutritional security of the people. The average productivity of pigeonpea has remained very low and stagnant for over five decades due to lack of genomic information and intensive breeding efforts. Previous SSR-based linkage maps of pigeonpea used inter-specific crosses due to low inter-varietal polymorphism. Here our aim was to construct a high density intra-specific linkage map using genic-SNP markers for mapping of major quantitative trait loci (QTLs) for key agronomic traits, including plant height, number of primary and secondary branches, number of pods, days to flowering and days to maturity in pigeonpea.ResultsA population of 186 F2:3 lines derived from an intra-specific cross between inbred lines 'Pusa Dwarf' and 'HDM04-1' was used to construct a dense molecular linkage map of 296 genic SNP and SSR markers covering a total adjusted map length of 1520.22 cM for the 11 chromosomes of the pigeonpea genome. This is the first dense intra-specific linkage map of pigeonpea with the highest genome length coverage. Phenotypic data from the F2:3 families were used to identify thirteen QTLs for the six agronomic traits. The proportion of phenotypic variance explained by the individual QTLs ranged from 3.18% to 51.4%. Ten of these QTLs were clustered in just two genomic regions, indicating pleiotropic effects or close genetic linkage. In addition to the main effects, significant epistatic interaction effects were detected between the QTLs for number of pods per plant.ConclusionsA large amount of information on transcript sequences, SSR markers and draft genome sequence is now available for pigeonpea. However, there is need to develop high density linkage maps and identify genes/QTLs for important agronomic traits for practical breeding applications. This is the first report on identification of QTLs for plant type and maturity traits in pigeonpea. The QTLs identified in this study provide a strong foundation for further validation and fine mapping for utilization in the pigeonpea improvement.

Project description:Pigeonpea productivity is greatly constrained by poor plant ideotype of existing Indian cultivars. Enhancing pigeonpea yield demands a renewed focus on restructuring the ideal plant type by using more efficient approaches like genomic tools. Therefore, the present study aims to identify and validate a set of QTLs/gene(s) presumably associated with various plant ideotype traits in pigeonpea. A total of 133 pigeonpea germplasms were evaluated along with four checks in the augmented design for various ideotype traits i.e. initiation of flowering (IF), days to 50% flowering (DFF), days to maturity (DM), plant height (PH), primary branches (PB), seeds per pod (SP) and pod length (PL). We observed significant genetic diversity in the germplasm lines for these traits. The genetic control of IF, DFF, DM and PH renders these traits suitable for detection of marker trait associations. By using residual maximum likelihood algorithm, we obtained appropriate variance-covariance structures for modeling heterogeneity, correlation of genetic effects and non-genetic residual effects. The estimates of genetic correlations indicated a strong association among earliness traits. The best linear unbiased prediction values were calculated for individual traits, and association analysis was performed in a panel of 95 diverse genotypes with 19 genic SSRs. Out of five QTL-flanking SSRs used here for validation, only ASSR295 could show significant association with FDR and Bonferroni corrections, and accounted for 15.4% IF, 14.2% DFF and 16.2% DM of phenotypic variance (PV). Remaining SSR markers (ASSR1486, ASSR206 and ASSR408) could not qualify false discovery rate (FDR) and Bonferroni criteria, hence declared as false positives. Additionally, we identified two highly significant SSR markers, ASSR8 and ASSR390 on LG 1 and LG 2, respectively. The SSR marker ASSR8 explained up to 22 and 11% PV for earliness traits and PB respectively, whereas ASSR390 controlled up to 17% PV for earliness traits. The validation and identification of new QTLs in pigeonpea across diverse genetic backgrounds brightens the prospects for marker-assisted selection to improve yield gains in pigeonpea.

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An improved draft of the pigeonpea (Cajanus cajan (L.) Millsp.) genome.

Publications

An improved draft of the pigeonpea (<i>Cajanus cajan</i> (L.) Millsp.) genome.

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