The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

Zhuang, Weijian; Chen, Hua; Yang, Meng; Wang, Jianping; Pandey, Manish K.; Zhuang, Weijian; Chang, Wen Chi; Zhang, Liangsheng; Zhang, Xingtan; Tang, Ronghua; Garg, Vanika; Wang, Xingjun; Tang, Haibao; Chow, Chi-Nga; Wang, Jinpeng; Deng, Ye; Wang, Depeng; Khan, Aamir W.; Yang, Qiang; Cai, Tiecheng; Bajaj, Prasad; Wu, Kangcheng; Guo, Bao‐Zhu; Zhang, Xinyou; Li, Jingjing; Liang, Fan; Hu, Jiang; Liao, Boshou; S, Liu; Chitikineni, Annapurna; Yan, Hansong; Zheng, Yanyan; Shan, Shiguang; Liu, Qinzheng; Xie, Dongyang; Wang, Zhenyi; Khan, Shahid Ali; Ali, Niaz; Zhao, Chuanzhi; Li, Xinguo; Luo, Ziliang; Zhang, Shubiao; Zhuang, Ruirong; Peng, Ze; Wang, Shuaiyin; Mamadou, Gandeka; Zhuang, Yuhui; Zhao, Zifan; Yu, Weichang; Xiong, Fei; Quan, Weipeng; Yüan, Ming; Liu, Yu; Zou, Huasong; Xia, Han; Zha, Li; Fan, Junpeng; Yu, Jigao; Xie, Wenping; Yuan, Jiaqing; Chen, Kun; Zhao, Shanshan; Chu, Wen-Ting; Chen, Yuting; Sun, Pengchuan; Meng, Fanbo; Zhuo, Tao; Zhao, Yuhao; Li, Chunjuan; Guo, He; Zhao, Yanni; Wang, Congcong; KaviKishor, Polavarapu B.; Pan, Rong-Long; Paterson, Andrew D.; Wang, Xiyin; Ming, Ray; Varshney, Rajeev K.

doi:10.1038/s41588-019-0402-2

Cited by 488 publications

(517 citation statements)

References 87 publications

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“…Base-calls were also derived computationally for four sequenced Arachis genomes: A. duranensis, A. ipaënsis (Bertioli et al 2016) and A. hypogaea varieties Tifrunner (Bertioli et al 2019), Shitouqi (Zhuang et al 2019), and Fuhuasheng . Base-calls from the genomic sequences were made by aligning flanking sequences plus the variant base, using two sequences per variant per locus, to the respective genome, using blastn (Altschul et al 1990).…”

Section: Diversity Phylogenetic and Network Analysismentioning

confidence: 99%

Genotypic characterization of the U.S. peanut core collection

Otyama

Kulkarni

Chamberlin

et al. 2020

Preprint

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Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin.The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions.the genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut's rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.

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Section: Diversity Phylogenetic and Network Analysismentioning

confidence: 99%

Genotypic characterization of the U.S. peanut core collection

Otyama

Kulkarni

Chamberlin

et al. 2020

Preprint

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“…Groundnut is an allotetraploid crop with a genome size of 2.7 Gbp and was domesticated in South and Central America from its wild ancestral species A. duranensis and A. ipaensis (Bertioli et al ., ; Chen et al ., ). The sequencing of both the subspecies of cultivated tetraploid groundnut along with other diverse accessions provided greater insights of evolution and domestication (Bertioli et al ., ; Chen et al ., ; Zhuang et al ., ). In Asia and Africa, groundnut is grown as major legume crop.…”

Section: Introductionmentioning

confidence: 99%

“…() reported two major QTLs controlling FSD, however, the use of F 2 generation with limited multiseason phenotyping does not help in precise detection of candidate genomic regions. With the availability of draft genome sequences of the diploid progenitors and tetraploid cultivated groundnut (Bertioli et al ., ; Chen et al ., ; Bertioli et al ., ; Chen et al ., ; Zhuang et al ., ), candidate gene discovery and marker development have become more precise and reliable. Of the available sequencing‐based approaches, QTL‐seq approach offers great benefits by identifying genomic region(s) and candidate genes leading to development of diagnostic markers.…”

Section: Introductionmentioning

confidence: 99%

Whole‐genome resequencing‐based QTL‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut

Kumar

Janila

Vishwakarma

et al. 2019

Plant Biotechnology Journal

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Summary The subspecies fastigiata of cultivated groundnut lost fresh seed dormancy (FSD) during domestication and human‐made selection. Groundnut varieties lacking FSD experience precocious seed germination during harvest imposing severe losses. Development of easy‐to‐use genetic markers enables early‐generation selection in different molecular breeding approaches. In this context, one recombinant inbred lines (RIL) population (ICGV 00350 × ICGV 97045) segregating for FSD was used for deploying QTL‐seq approach for identification of key genomic regions and candidate genes. Whole‐genome sequencing (WGS) data (87.93 Gbp) were generated and analysed for the dormant parent (ICGV 97045) and two DNA pools (dormant and nondormant). After analysis of resequenced data from the pooled samples with dormant parent (reference genome), we calculated delta‐SNP index and identified a total of 10,759 genomewide high‐confidence SNPs. Two candidate genomic regions spanning 2.4 Mb and 0.74 Mb on the B05 and A09 pseudomolecules, respectively, were identified controlling FSD. Two candidate genes—RING‐H2 finger protein and zeaxanthin epoxidase—were identified in these two regions, which significantly express during seed development and control abscisic acid (ABA) accumulation. QTL‐seq study presented here laid out development of a marker, GMFSD1, which was validated on a diverse panel and could be used in molecular breeding to improve dormancy in groundnut.

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“…The breeding efforts mainly focus on productivity, disease and insect resistance, oil quality etc. Genomics-assisted breeding has been successfully employed [1,2] with the development of the genomic resources including the genome sequence of the cultivated allotetraploid peanut [3,4]. Apart from the genome, the epigenome also influences the gene function and the phenotype [5].…”

Section: Introductionmentioning

confidence: 99%

DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)

et al. 2020

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Objective: Low DNA sequence polymorphism despite enormous phenotypic variations in peanut indicates the possible role of epigenetic variations. An attempt was made to analyze genome-wide DNA methylation pattern and its influence on gene expression across 11 diverse genotypes of peanut. Results:The genotypes were subjected to bisulfite sequencing after 21 days of sowing (DAS). CHG regions showed the highest (30,537,376) DNA methylation followed by CpG (30,356,066) and CHH (15,993,361) across 11 genotypes. The B sub-genome exhibited higher DNA methylation sites (46,294,063) than the A sub-genome (30,415,166). Overall, the DNA methylation was more frequent in inter-genic regions than in the genic regions. The genes showing altered methylation and expression between the parent (TMV 2) and its EMS-derived mutant (TMV 2-NLM) were identified. Foliar disease resistant genotypes showed significant differential DNA methylation at 766 sites corresponding to 25 genes. Of them, two genes (Arahy.1XYC2X on chromosome 01 and Arahy.00Z2SH on chromosome 17) coding for senescence-associated protein showed differential expression with resistant genotypes recording higher fragments per kilobase of transcript per million mapped reads (FPKM) at their epialleles. Overall, the study indicated the variation in the DNA methylation pattern among the diverse genotypes of peanut and its influence of gene expression.

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The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

Cited by 488 publications

References 87 publications

Genotypic characterization of the U.S. peanut core collection

Genotypic characterization of the U.S. peanut core collection

Whole‐genome resequencing‐based QTL‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut

DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.)

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