Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)

Lu, Qing; Li, Haifen; Hong, Yanbin; Zhang, Guo‐Qiang; Wen, Shaoqing; Li, Xingyu; Guiyuan, Zhou; Li, Shaoxiong; Líu, Hao; Liu, Haiyan; Liu, Zhong‐Jian; Varshney, Rajeev K.; Chen, Xiaoping; Liang, Xuanqiang

doi:10.3389/fpls.2018.00604

Cited by 42 publications

(47 citation statements)

References 101 publications

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“…duranensis . FAR1 has been linked with skotomorphogenesis and photomorphogenesis in higher plants and its expansion might be related with the fructification process in peanuts (Chen et al, 2016;Lu et al, 2018). Unlike the above-mentioned expansions of MADS TFs in Am.…”

Section: Resultsmentioning

confidence: 99%

Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae)

Moharana

Venancio

2019

Preprint

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AbstractTranscription factors (TF) are essential for proper plant growth and development. Several legumes, particularly soybean, are rich sources of protein and oil, with great impact in the economy of several countries. Here we report a phylogenomic analysis of major TF families in legumes and their potential association with important traits such as nitrogen fixation and seed development. We used TF DNA-binding domains to systematically screen the genomes of 15 legume and 5 non-legume species. The percentage of TFs ranged from 3-8% of the gene complements. TF orthologous groups (OG) in extant species were used to estimate OG sizes in ancestor nodes using a gene birth-death model, which allowed us to identify lineage-specific expansions. Together, OG analysis and rate of synonymous substitutions (Ks) between gene pairs show that major TF expansions are strongly associated with known whole-genome duplication (WGD) events in the legume (∼58 mya) and Glycine (∼13 mya) lineages, which account for a large fraction of the Ph. vulgaris and Gl. max TF repertoires. Out of the 3407 Gl. max TFs, 1808 and 676 can be traced back to a single homeolog in Ph. vulgaris and Vi vinifera, respectively. We found a trend for TFs expanded in legumes to be preferentially transcribed in roots and nodules, suggesting their recruitment early in the evolution of nodulation in the legume clade. We also found TF expansions in the Glycine WGD that were followed by gene loss in the wild soybean Gl. soja, including genes located within important quantitative trait loci. Together, our findings strongly support the roles of two WGDs in shaping the TF repertoires in the legume and Glycine lineages, which are likely related to important aspects of legume and soybean biology.

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Section: Resultsmentioning

confidence: 99%

Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae)

Moharana

Venancio

2019

Preprint

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“…SNP arrays and whole‐genome resequencing (WGRS) are the advanced NGS technologies producing maximum data points for high‐density genetic mapping. Both peanut progenitor genome sequences, A. duranensis (A genome) and A. ipaensis (B genome) (Bertioli et al , ; Chen et al , ; Lu et al , ), are available with annotations. Recently, assemblies of reference genome have also become available for cultivated peanut (Bertioli et al , ; Chen et al , ; Zhuang et al , ) and will increase the efficiency of such studies in the future.…”

Section: Discussionmentioning

confidence: 99%

“…In peanut, the genetic dissection of important traits has been carried out using QTL mapping of segregating RIL populations derived from biparental crosses (Agarwal et al , ; Chavarro et al , ; Lu et al , ; Luo et al , ; Pandey et al , ). The NAM design has been successful in several crops to exploit the benefits of both joint linkage analysis and association mapping simultaneously in rapeseed and maize (Hu et al , ; McMullen et al , ) to dissect the genetic basis of complex quantitative traits.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, a major QTL identified on chromosome A05 for seed number per pod using a biparental cross (Chen et al , ). QTL meta‐analysis using consensus map narrowed down the QTL region to 0.7 cM on chromosome A05 (Lu et al , ). In this study, seven and four STAs identified in NAM‐T and NAM‐F, respectively, co‐located in QTL regions of PW and SW in both seasons on chromosomes A05.…”

Section: Discussionmentioning

confidence: 99%

“…Availability of a high‐density genotyping platform with uniformly distributed genomewide genetic markers is critical for high‐resolution genetic dissection of complex traits and tracking the favourable alleles in a breeding population (Pandey et al , ; Pandey et al , ; Varshney et al , ). Reference genome sequences of both wild diploid progenitors A. ipaensis and A. duranensis (Bertioli et al , ; Chen et al , ; Lu et al , ), as well as allotetraploid cultivated peanut A. hypogaea (Bertioli et al , ; Chen et al , ; Zhuang et al , ), have recently been assembled by the international peanut community and are important resources for sequence‐based trait mapping and candidate gene discovery. This has also facilitated the development of high‐resolution SNP arrays in peanut (Clevenger et al , ; Pandey et al , ), which have shown great utility in fine trait mapping in other crops such as rice (Thomson et al , ), soybean (Xavier et al , ), maize (Yan et al , ), wheat (Wang et al , ), chickpea (Roorkiwal et al , ) and pigeonpea (Saxena et al , ; Yadav et al , ).…”

Section: Introductionmentioning

confidence: 99%

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Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

Gangurde

Wang

Shasidhar

et al. 2019

Plant Biotechnology Journal

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email baozhu.guo@usda.gov (B. G.); Tel 91-40-30713345; fax 91-40-30713074; email r.k.varshney@cgiar.org (R. K. V.)) † These authors contributed equally to this study. SummaryMultiparental genetic mapping populations such as nested-association mapping (NAM) have great potential for investigating quantitative traits and associated genomic regions leading to rapid discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two NAM populations, NAM_Tifrunner and NAM_Florida-07, were used for dissecting genetic control of 100-pod weight (PW) and 100-seed weight (SW) in peanut. Two high-density SNP-based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner and NAM_Florida-07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8 major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effect QTLs for PW and SW, respectively, in NAM_Florida-07. Most of the QTLs associated with PW and SW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide association study (GWAS) analysis identified 19 and 28 highly significant SNP-trait associations (STAs) in NAM_Tifrunner and 11 and 17 STAs in NAM_Florida-07 for PW and SW, respectively. These significant STAs were co-localized, suggesting that PW and SW are co-regulated by several candidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstrates the utility of NAM population for genetic dissection of complex traits and performing highresolution trait mapping in peanut.

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Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Reynolds,

Mumey,

Strnadova‐Neeley

et al. 2024

Appl Plant Sci

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PremiseThe genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics.MethodsHere, the problem of intra‐ and inter‐genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k‐mer composition and frequency with a range of k‐mer sizes. In this approach, no subgenome‐specific k‐mers are identified; rather, whole‐chromosome k‐mer subspaces were utilized.ResultsGiven chromosome‐scale genome assemblies with sufficient subgenome‐specific repetitive element content, literature‐verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto‐ from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k‐mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics‐based method.DiscussionThe easily implementable and highly computationally efficient MinHashing‐based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy‐type subgenomic assignments. In cases where subgenome‐specific repeat signal may not be adequate given a chromosomes' global k‐mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

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Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)

Cited by 42 publications

References 101 publications

Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae)

Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae)

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

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