Genome‐wide structural and functional features of single nucleotide polymorphisms revealed from the whole genome resequencing of 179 accessions of <i>Arachis</i>

Bhat, Ramesh; Shirasawa, Kenta; Chavadi, S. D.

doi:10.1111/ppl.13623

Cited by 7 publications

(3 citation statements)

References 41 publications

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“…These variants can be all used in molecular marker-assisted breeding. But the number of SNPs in Monticola and Pingdu9616 was significantly less than the studies conducted by Bhat et al [30] which indicated that wild and the cultivated species are obviously different in genotype. Compared with other studies in gene family, most gene family such as TFs from 57 families and GeBP family were identified less in Monticola and Pingdu9616 than Fuhuasheng [15].…”

Section: Discussionmentioning

confidence: 59%

Full-Length Transcriptome Analysis of Cultivated and Wild Tetraploid Peanut

Song¹,

Yu²,

Li³

et al. 2023

Phyton

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The high-quality genomes and large-scale full-length cDNA sequences of allotetraploid peanuts have been sequenced and released, which has accelerated the functional genomics and molecular breeding research of peanut. In order to understand the difference in the transcriptional levels of wild and cultivated peanuts. In this study, we integrated of second-and third-generation sequencing technologies to sequence full-length transcriptomes in peanut cv. Pingdu9616 and its putative ancestor Arachis monticola. The RNA extracted from six different tissues (i.e., roots, stems, leaves, flowers, needles and pods) were sampled at 20 days after flowering. A total of 31,764 and 33,981 high-quality transcripts were obtained from Monticola and Pingdu9616, respectively. The number of alternative splicing, the unit point mutation of variable adenylation, the number of open reading frames and the two-site mutation were identified in Pingdu9616 more than in Monticola, but the three-site mutation in Pingdu9616 was lower than in Monticola. 1,691 LncRNAs, and 4,000 bp of maximum length of LncRNA was identified in Monticola and Pingdu9616. Furthermore, comparative analysis between transcript data shown that 56 transcription factor families were involved in Monticola, and Pingdu9616 and the number of transcription factors in Pingdu9616 was higher than that in Monticola, the number of expressed genes estimated in flower, root, young pod and leaf organs was higher in Monticola than Pingdu9616. Over all, our study provided a valuable resource of large-scale full-length transcripts for further research of the molecular breeding and functional analysis of genes.

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Section: Discussionmentioning

confidence: 59%

Full-Length Transcriptome Analysis of Cultivated and Wild Tetraploid Peanut

Song¹,

Yu²,

Li³

et al. 2023

Phyton

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“…Arahy.W1P0U6 and Araip.SJ8UT genes though code for disease resistance proteins, previous reports showed their induction under drought stress in peanut (Khan et al 2020;Deng et al 2018) and maize (Yang et al 2021). The SNP at Ah02_1558700 was found to be rare since it was detected only between TMV 2 and TMV 2-NLM but not among any of the 179 accessions of peanut (Bhat et al 2022). Other two genes, Arahy.H3LZVP and Arahy.23PCL8 in the same QTL region code for mediator of RNA polymerase protein and protein kinase super-family protein, respectively.…”

Section: Discussionmentioning

confidence: 84%

Genetic mapping of drought tolerance traits phenotyped under varying drought stress environments in peanut (Arachis hypogaea L.)

et al. 2022

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drought tolerance traits for the rainy and post-rainy seasons at Dharwad and post-rainy seasons at Tirupati, and employed for single marker analysis, composite interval mapping and multiple QTL mapping. Of the 305 significant marker-trait associations for the 11 traits, only 21 were of major effect for pod yield per plant (PYPP), specific dry weight at 70 days after sowing (SDW_70) and specific leaf area at 70 DAS (SLA_70). Three major main effect QTLs were identified for PYPP with the highest phenotypic variance explained (PVE) of 10.5%. Nine QTLs with the highest PVE of 18.4% were identified for SDW_70, of which four QTLs were also governing SLA_70 with Abstract Genomic regions governing water deficit stress tolerance were identified in peanut using a recombinant inbred line (RIL) population derived from an elite variety TMV 2 and its narrow leaf mutant TMV 2-NLM, which was evaluated over six-seasons at Dharwad (non-stress) and Tirupati (water-stress) in India. Stress condition could differentiate the RILs much better than the non-stress condition for the physiological traits. A linkage map with 700 markers was used to identify the quantitative trait loci (QTLs). Three sets of best linear unbiased predictions (BLUPs) were estimated for the

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“…Such improvements have facilitated the rapid sequencing of the whole genomes of a large number of plant species, leading to the identification and characterization of new and important genes, alleles, and molecular markers. Bhat et al (2022) used the whole-genome resequencing (WGRS) data obtained from 178 peanut genotypes to identify more than 4.3 million SNPs. Of these, 2488 SNPs had a high impact due to the gain of stop codons, variations in splice acceptors and splice donors, and the loss of start codons.…”

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confidence: 99%