A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.)

Singh, S. P.; Mahato, Ajay Kumar; Jayaswal, Pawan Kumar; Singh, Nisha; Dheer, Meenakshi; Goel, Preeti; Raje, R. S.; Yasin, Jeshima Khan; Sreevathsa, Rohini; Rai, Vandna; Gaikwad, Kishor; Singh, Nagendra

doi:10.1038/s41598-020-61889-0

Cited by 27 publications

(18 citation statements)

References 46 publications

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“…Considering the correlation between seed yield per plant and other characters, it was found that seed yield was positively correlated with number of pods per plant, number of seeds per pod and number of primary branches. Similar report was given by Bhadru (2010).The high yielding lines selected and studied for their molecular diversity using 62K SNP chip has confirmed the variations and correlations among the selected contrasting breeding lines (Singh et al, 2020). Hence, these characters namely seeds per pod and hundred seed weight have to be given importance during the selection programme to improve the yield potential of the crop.…”

Section: Correlation and Path Analysissupporting

confidence: 77%

“…Characterization and evaluation of available germplasm for different agro-morphological and biochemical traits is necessary to identify the effect of different genes on the phenotypes. We have already developed and evaluated high yielding lines in pigeon pea (Arumugam et al, 2018), identified diverse markers and validated the developed high yielding lines (Singh et al, 2020), genes and genes network were also being cracked (Chaudhary et al, 2017;Yasin et al, 2018;Yasin et al, 2019). In continuation to that, the present study was carried out with an objective to characterize two hundred selected pre-breeding accessions for the qualitative traits to estimate the genetic variability, heritability, coefficient of variation and character association analysis.…”

Section: Introductionmentioning

confidence: 98%

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Assessment of Genetic Variability and Traits Association in Pigeonpea [Cajanus cajan (L.) Millsp.] Germplasm

Vanniarajan¹,

Magudeeswari²,

Gowthami³

et al. 2021

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Background: Pigeon pea is an important dietary protein source for humans but the production was constrained by various biotic and abiotic factors. Breeding strategies were followed to improve yield and developing high yielding varieties but at the same time utilization of genetic resources have declined. Pigeon pea is native to India with huge natural genetic variability in the local germplasm and its wild relatives. So it is necessary to identify and select breeding material from germplasm with considerable genetic and morphological variability to utilize in breeding programmes. As an initial study, 200 pre-breeding lines developed were evaluated for morphological variability patterns.Methods: A total of two hundred lines selected from F4 generation of pigeon pea developed at ICAR-NBPGR were evaluated in Randomized Block design (RBD) during 2014-2015 kharif season under Indo-Swiss collaboration in Biotechnology at Agricultural College and Research Institute, Madurai (TNAU). The accessions found to be superior in seed yield than the local check APK1were forwarded to the next generation (2015-2016) for assessment of genetic variability, heritability, genetic advance and association studies.Result: Qualitative traits were evaluated and variation in leaflet shape, stem colour, pattern of streaks and base seed colour were observed. All tested lines expressed greater variability for most of the traits. Maximum coefficient of variation was observed for number of pods per plant followed by number of primary branches per plant. Selection of traits with moderate heritability coupled with high genetic advance like number of pods per plant, number of primary branches per plant could help in crop improvement program. Seed yield was positively correlated with number of seeds per pod, number of pods per plant and hundred seed weight. Potential genetic stocks and donors for high yield were selected based on hundred seed weight and seeds per pod. The accessions superior in number of pods and seed yield than check were forwarded to next generation for assessment. The identified trait-specific accessions will help in future breeding program.

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Section: Correlation and Path Analysissupporting

confidence: 77%

Section: Introductionmentioning

confidence: 98%

Assessment of Genetic Variability and Traits Association in Pigeonpea [Cajanus cajan (L.) Millsp.] Germplasm

Vanniarajan¹,

Magudeeswari²,

Gowthami³

et al. 2021

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“…Legume genomes are rich in SNPs. Saturated map of SNPs were reported in legumes like vigna (55) and In pigeonpea (56). Of which highest haplotype desnsity of 0.7380 was reported for serine threonine kinase coding disease resistance gene (56) which was identified as an important miR target in the present ivestigation.…”

Section: Discussionmentioning

confidence: 93%

Genome wide in-silico miRNA and target network prediction from stress responsive Horsegram (Macrotyloma uniflorum) accessions

Yasin

Mishra

Pillai

et al. 2020

Sci Rep

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Horsegram (Macrotyloma uniflorum (Lam.) Verdc.) is a drought hardy food and fodder legume of Indo-African continents with diverse germplasm sources demonstrating alternating mechanisms depicting contrasting adaptations to different climatic zones. Tissue specific expression of genes contributes substantially to location specific adaptations. Regulatory networks of such adaptive genes are elucidated for downstream translational research. MicroRNAs are small endogenous regulatory RNAs which alters the gene expression profiles at a particular time and type of tissue. Identification of such small regulatory RNAs in low moisture stress hardy crops can help in cross species transfer and validation confirming stress tolerance ability. This study outlined prediction of conserved miRNAs from transcriptome shotgun assembled sequences and EST sequences of horsegram. We could validate eight out of 15 of the identified miRNAs to demonstrate their role in deficit moisture stress tolerance mechanism of horsegram variety Paiyur1 with their target networks. The putative mumiRs were related to other food legumes indicating the presence of gene regulatory networks. Differential miRNA expression among drought specific tissues indicted the probable energy conservation mechanism. Targets were identified for functional characterization and regulatory network was constructed to find out the probable pathways of post-transcriptional regulation. The functional network revealed mechanism of biotic and abiotic stress tolerance, energy conservation and photoperiod responsiveness.

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“…"C": cluster (colour figure online) (Singh et al 2016;Roorkiwal et al 2013;Saxena et al 2012;Kassa et al 2012). Similarly, in the case of pigeonpea, a number of datasets have been produced using NGS (Varshney et al 2012) and Cajanus SNP array (Saxena et al 2018;Singh et al 2020). These datasets have been used in several studies, for instance GBS for trait mapping (Saxena et al 2017a(Saxena et al , b, c, 2020, WGS for trait mapping, gene discovery, diversity, evolutionary analysis (Varshney et al 2017;Singh et al 2016), SNP array data for diversity analysis, trait mapping (Yadav et al 2019), etc.…”

Section: Discussionmentioning

confidence: 99%

A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea

et al. 2020

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Fusarium wilt (FW) and sterility mosaic diseases (SMD) are key biotic constraints to pigeonpea production. Occurrence of these two diseases in congenial conditions is reported to cause complete yield loss in susceptible pigeonpea cultivars. Various studies to elucidate genomic architecture of the two traits have revealed significant marker–trait associations for use in breeding programs. However, these DNA markers could not be used effectively in genomics-assisted breeding for developing FW and SMD resistant varieties primarily due to pathogen variability, location or background specificity, lesser phenotypic variance explained by the reported QTL and cost-inefficiency of the genotyping assays. Therefore, in the present study, a novel approach has been used to develop a diagnostic kit for identification of suitable FW and SMD resistant lines. This kit was developed with 10 markers each for FW and SMD resistance. Investigation of the diversity of these loci has shown the role of different alleles in different resistant genotypes. Two genes (C.cajan_03691 and C.cajan_18888) for FW resistance and four genes (C.cajan_07858, C.cajan_20995, C.cajan_21801 and C.cajan_17341) for SMD resistance have been identified. More importantly, we developed a customized and cost-effective Kompetitive allele-specific PCR genotyping assay for the identified genes in order to encourage their downstream applications in pigeonpea breeding programs. The diagnostic marker kit developed here will offer great strength to pigeonpea varietal development program, since the resistance against these two diseases is essentially required for nominating an improved line in varietal release pipeline.

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A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.)

Cited by 27 publications

References 46 publications

Assessment of Genetic Variability and Traits Association in Pigeonpea [Cajanus cajan (L.) Millsp.] Germplasm

Assessment of Genetic Variability and Traits Association in Pigeonpea [Cajanus cajan (L.) Millsp.] Germplasm

Genome wide in-silico miRNA and target network prediction from stress responsive Horsegram (Macrotyloma uniflorum) accessions

A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea

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