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Massa AN, Sobolev VS, Faustinelli PC, Tallury SP, Stalker HT, Lamb MC, Arias RS. Genetic diversity, disease resistance, and environmental adaptation of Arachis duranensis L.: New insights from landscape genomics. PLoS One 2024; 19:e0299992. [PMID: 38625995 PMCID: PMC11020403 DOI: 10.1371/journal.pone.0299992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/19/2024] [Indexed: 04/18/2024] Open
Abstract
The genetic diversity that exists in natural populations of Arachis duranensis, the wild diploid donor of the A subgenome of cultivated tetraploid peanut, has the potential to improve crop adaptability, resilience to major pests and diseases, and drought tolerance. Despite its potential value for peanut improvement, limited research has been focused on the association between allelic variation, environmental factors, and response to early (ELS) and late leaf spot (LLS) diseases. The present study implemented a landscape genomics approach to gain a better understanding of the genetic variability of A. duranensis represented in the ex-situ peanut germplasm collection maintained at the U.S. Department of Agriculture, which spans the entire geographic range of the species in its center of origin in South America. A set of 2810 single nucleotide polymorphism (SNP) markers allowed a high-resolution genome-wide characterization of natural populations. The analysis of population structure showed a complex pattern of genetic diversity with five putative groups. The incorporation of bioclimatic variables for genotype-environment associations, using the latent factor mixed model (LFMM2) method, provided insights into the genomic signatures of environmental adaptation, and led to the identification of SNP loci whose allele frequencies were correlated with elevation, temperature, and precipitation-related variables (q < 0.05). The LFMM2 analysis for ELS and LLS detected candidate SNPs and genomic regions on chromosomes A02, A03, A04, A06, and A08. These findings highlight the importance of the application of landscape genomics in ex situ collections of peanut and other crop wild relatives to effectively identify favorable alleles and germplasm for incorporation into breeding programs. We report new sources of A. duranensis germplasm harboring adaptive allelic variation, which have the potential to be utilized in introgression breeding for a single or multiple environmental factors, as well as for resistance to leaf spot diseases.
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Affiliation(s)
- Alicia N. Massa
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
| | - Victor S. Sobolev
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
| | - Paola C. Faustinelli
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
| | - Shyamalrau P. Tallury
- Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, Georgia, United States of America
| | - H. Thomas Stalker
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Marshall C. Lamb
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
| | - Renee S. Arias
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
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2
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Gao H, Ma J, Zhao Y, Zhang C, Zhao M, He S, Sun Y, Fang X, Chen X, Ma K, Pang Y, Gu Y, Dongye Y, Wu J, Xu P, Zhang S. The MYB Transcription Factor GmMYB78 Negatively Regulates Phytophthora sojae Resistance in Soybean. Int J Mol Sci 2024; 25:4247. [PMID: 38673832 PMCID: PMC11050205 DOI: 10.3390/ijms25084247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Phytophthora root rot is a devastating disease of soybean caused by Phytophthora sojae. However, the resistance mechanism is not yet clear. Our previous studies have shown that GmAP2 enhances sensitivity to P. sojae in soybean, and GmMYB78 is downregulated in the transcriptome analysis of GmAP2-overexpressing transgenic hairy roots. Here, GmMYB78 was significantly induced by P. sojae in susceptible soybean, and the overexpressing of GmMYB78 enhanced sensitivity to the pathogen, while silencing GmMYB78 enhances resistance to P. sojae, indicating that GmMYB78 is a negative regulator of P. sojae. Moreover, the jasmonic acid (JA) content and JA synthesis gene GmAOS1 was highly upregulated in GmMYB78-silencing roots and highly downregulated in overexpressing ones, suggesting that GmMYB78 could respond to P. sojae through the JA signaling pathway. Furthermore, the expression of several pathogenesis-related genes was significantly lower in GmMYB78-overexpressing roots and higher in GmMYB78-silencing ones. Additionally, we screened and identified the upstream regulator GmbHLH122 and downstream target gene GmbZIP25 of GmMYB78. GmbHLH122 was highly induced by P. sojae and could inhibit GmMYB78 expression in resistant soybean, and GmMYB78 was highly expressed to activate downstream target gene GmbZIP25 transcription in susceptible soybean. In conclusion, our data reveal that GmMYB78 triggers soybean sensitivity to P. sojae by inhibiting the JA signaling pathway and the expression of pathogenesis-related genes or through the effects of the GmbHLH122-GmMYB78-GmbZIP25 cascade pathway.
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Affiliation(s)
- Hong Gao
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Jia Ma
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yuxin Zhao
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Chuanzhong Zhang
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Ming Zhao
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Shengfu He
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yan Sun
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Xin Fang
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Xiaoyu Chen
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Kexin Ma
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yanjie Pang
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yachang Gu
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Yaqun Dongye
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Junjiang Wu
- Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences/Key Laboratory of Soybean Cultivation of Ministry of Agriculture, Harbin 150030, China;
| | - Pengfei Xu
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
| | - Shuzhen Zhang
- Soybean Research Institute of Northeast Agricultural University/Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin 150030, China; (H.G.); (J.M.); (Y.Z.); (C.Z.); (M.Z.); (S.H.); (Y.S.); (X.F.); (X.C.); (K.M.); (Y.P.); (Y.G.); (Y.D.)
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3
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Bhat RS, Shirasawa K, Chavadi SD. Genome-wide structural and functional features of single nucleotide polymorphisms revealed from the whole genome resequencing of 179 accessions of Arachis. PHYSIOLOGIA PLANTARUM 2022; 174:e13623. [PMID: 35018642 DOI: 10.1111/ppl.13623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Peanut being an important food, oilseed and fodder crop worldwide, its genetic improvement currently relies on genomics-assisted breeding (GAB). Since the level of marker polymorphism is limited in peanut, the availability of a large number of DNA markers is the prerequisite for GAB. Therefore, we detected 4,309,724 single nucleotide polymorphisms (SNPs) from the whole genome re-sequencing (WGRS) data of 178 peanut accessions along with the reference genome sequence of Tifrunner. SNPs were analyzed for their structural and functional features to conclude on their utility and employability in genetic and genomic studies. ISATGR278-18, a synthetic amphidiploid, showed the highest number of SNPs (2,505,266), while PI_628538 recorded the lowest number (19,058) of SNPs. A03 showed the highest number of SNPs, while B08 recorded the lowest number of SNPs. The number of accessions required to record 50% of the total SNPs varied from 11 to 13 across the chromosomes. The rate of transitions was more than that of transversions. Among the various chromosomal contexts, intergenic and intronic regions carried more SNPs than the exonic regions. SNP impact analysis indicated 2488 SNPs with high impact due to gain of stop codons, variations in splice acceptors and splice donors, and loss of start codons. Of the 4,309,723 SNPs, 46,087 had the highest polymorphic information content (PIC) of 0.375. As an illustration of application, the drought-tolerant accession C76-16 was compared with A72 (an accession with high-stress rating) to identify 637,833 SNPs, of which 418 had high impact substitutions. Overall, these structural and functional features of the SNPs will be of immense importance for their utility in genetic and genomic studies in peanut.
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Affiliation(s)
- Ramesh S Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Shwetha D Chavadi
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
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4
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Massa AN, Bressano M, Soave JH, Buteler MI, Seijo G, Sobolev VS, Orner VA, Oddino C, Soave SJ, Faustinelli PC, de Blas FJ, Lamb MC, Arias RS. Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study. PeerJ 2021; 9:e10581. [PMID: 33575123 PMCID: PMC7849506 DOI: 10.7717/peerj.10581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.
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Affiliation(s)
- Alicia N Massa
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | - Marina Bressano
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Juan H Soave
- Criadero El Carmen, General Cabrera, Córdoba, Argentina
| | | | - Guillermo Seijo
- Instituto de Botánica del Nordeste (IBONE, CONICET-UNNE) and Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | | | - Valerie A Orner
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | | | - Sara J Soave
- Criadero El Carmen, General Cabrera, Córdoba, Argentina
| | | | - Francisco J de Blas
- Instituto Multidisciplinario de Biología Vegetal-(IMBIV-CONICET-UNC), Córdoba, Argentina
| | - Marshall C Lamb
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | - Renee S Arias
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
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5
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Crosslinked Recombinant-Ara h 1 Catalyzed by Microbial Transglutaminase: Preparation, Structural Characterization and Allergic Assessment. Foods 2020; 9:foods9101508. [PMID: 33096617 PMCID: PMC7590132 DOI: 10.3390/foods9101508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 01/01/2023] Open
Abstract
As the one of the major allergens in peanut, the allergenicity of Ara h 1 is influenced by its intrinsic structure, which can be modified by different processing. However, molecular information in this modification has not been clarified to date. Here, we detected the influence of microbial transglutaminase (MTG) catalyzed cross-linking on the recombinant peanut protein Ara h 1 (rAra h 1). Electrophoresis and spectroscopic methods were used to analysis the structural changes. The immunoreactivity alterations were characterized by enzyme linked immunosorbent assay (ELISA), immunoblotting and degranulation test. Structural features of cross-linked rAra h 1 varied at different reaction stages. Hydrogen bonds and disulfide bonds were the main molecular forces in polymers induced by heating and reducing. In MTG-catalyzed cross-linking, ε-(γ-glutamyl) lysine isopeptide bonds were formed, thus inducing a relatively stable structure in polymers. MTG catalyzed cross-linking could modestly but significantly reduce the immunoreactivity of rAra h 1. Decreased content of conserved secondary structures led to a loss of protection of linear epitopes. Besides, the reduced surface hydrophobic index and increased steric hindrance of rAra h 1 made it more difficult to bind with antibodies, thus hindering the subsequent allergic reaction.
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Chavarro C, Chu Y, Holbrook C, Isleib T, Bertioli D, Hovav R, Butts C, Lamb M, Sorensen R, A Jackson S, Ozias-Akins P. Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences. G3 (BETHESDA, MD.) 2020; 10:2297-2315. [PMID: 32398236 PMCID: PMC7341151 DOI: 10.1534/g3.120.401147] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022]
Abstract
Although seed and pod traits are important for peanut breeding, little is known about the inheritance of these traits. A recombinant inbred line (RIL) population of 156 lines from a cross of Tifrunner x NC 3033 was genotyped with the Axiom_Arachis1 SNP array and SSRs to generate a genetic map composed of 1524 markers in 29 linkage groups (LG). The genetic positions of markers were compared with their physical positions on the peanut genome to confirm the validity of the linkage map and explore the distribution of recombination and potential chromosomal rearrangements. This linkage map was then used to identify Quantitative Trait Loci (QTL) for seed and pod traits that were phenotyped over three consecutive years for the purpose of developing trait-associated markers for breeding. Forty-nine QTL were identified in 14 LG for seed size index, kernel percentage, seed weight, pod weight, single-kernel, double-kernel, pod area and pod density. Twenty QTL demonstrated phenotypic variance explained (PVE) greater than 10% and eight more than 20%. Of note, seven of the eight major QTL for pod area, pod weight and seed weight (PVE >20% variance) were attributed to NC 3033 and located in a single linkage group, LG B06_1. In contrast, the most consistent QTL for kernel percentage were located on A07/B07 and derived from Tifrunner.
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Affiliation(s)
- Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793
| | - Corley Holbrook
- USDA- Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793
| | - Thomas Isleib
- Department of Crop Science, North Carolina State University, P.O. Box 7629, Raleigh, NC 27695
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Ran Hovav
- Department of Field and Vegetable Crops, Plant Sciences Institute, ARO (Volcani Center), Bet Dagan, Israel, and
| | - Christopher Butts
- USDA- Agricultural Research Service, National Peanut Research Laboratory, Dawson, GA 39842
| | - Marshall Lamb
- USDA- Agricultural Research Service, National Peanut Research Laboratory, Dawson, GA 39842
| | - Ronald Sorensen
- USDA- Agricultural Research Service, National Peanut Research Laboratory, Dawson, GA 39842
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793,
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Desmae H, Janila P, Okori P, Pandey MK, Motagi BN, Monyo E, Mponda O, Okello D, Sako D, Echeckwu C, Oteng‐Frimpong R, Miningou A, Ojiewo C, Varshney RK. Genetics, genomics and breeding of groundnut ( Arachis hypogaea L.). PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:425-444. [PMID: 31598026 PMCID: PMC6774334 DOI: 10.1111/pbr.12645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 05/04/2023]
Abstract
Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.
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Affiliation(s)
- Haile Desmae
- International Crop Research Institute for the Semi‐Arid Tropics (ICRISAT)BamakoMali
| | | | | | | | | | | | - Omari Mponda
- Division of Research and Development (DRD)Tanzania Agricultural Research Institute (TARI) ‐ NaliendeleMtwaraTanzania
| | - David Okello
- National Agricultural Research Organization (NARO)EntebbeUganda
| | | | | | | | - Amos Miningou
- Institut National d'Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
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8
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Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut. Genes (Basel) 2019; 10:genes10070536. [PMID: 31311183 PMCID: PMC6679159 DOI: 10.3390/genes10070536] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/29/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut.
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9
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Bertioli DJ, Jenkins J, Clevenger J, Dudchenko O, Gao D, Seijo G, Leal-Bertioli SCM, Ren L, Farmer AD, Pandey MK, Samoluk SS, Abernathy B, Agarwal G, Ballén-Taborda C, Cameron C, Campbell J, Chavarro C, Chitikineni A, Chu Y, Dash S, El Baidouri M, Guo B, Huang W, Kim KD, Korani W, Lanciano S, Lui CG, Mirouze M, Moretzsohn MC, Pham M, Shin JH, Shirasawa K, Sinharoy S, Sreedasyam A, Weeks NT, Zhang X, Zheng Z, Sun Z, Froenicke L, Aiden EL, Michelmore R, Varshney RK, Holbrook CC, Cannon EKS, Scheffler BE, Grimwood J, Ozias-Akins P, Cannon SB, Jackson SA, Schmutz J. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 2019; 51:877-884. [PMID: 31043755 DOI: 10.1038/s41588-019-0405-z] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/28/2019] [Indexed: 12/24/2022]
Abstract
Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.
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Affiliation(s)
- David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA. .,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA. .,Department of Crop and Soil Science, University of Georgia, Athens, GA, USA.
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Josh Clevenger
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.,Department of Crop and Soil Science, University of Georgia, Athens, GA, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (CONICET-UNNE), Corrientes, Argentina.,FACENA, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.,Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - Longhui Ren
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, USA
| | | | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sergio S Samoluk
- Instituto de Botánica del Nordeste (CONICET-UNNE), Corrientes, Argentina.,FACENA, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Gaurav Agarwal
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | | | | | | | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ye Chu
- Department of Horticulture, University of Georgia, Tifton, GA, USA
| | - Sudhansu Dash
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Moaine El Baidouri
- UMR5096, Laboratoire Génome et Développement des Plantes, CNRS, Perpignan, France.,UMR5096, Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France
| | - Baozhu Guo
- Crop Protection and Management Research Unit, US Department of Agriculture, Agricultural Research Service, Tifton, GA, USA
| | - Wei Huang
- Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Corporate R&D, LG Chem, Seoul, Republic of Korea
| | - Walid Korani
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Sophie Lanciano
- UMR5096, Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France.,UMR232, Diversité, Adaptation et Développement des Plantes, IRD, Montpellier, France.,UMR232, Diversité, Adaptation et Développement des Plantes, Université de Montpellier, Montpellier, France
| | - Christopher G Lui
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Marie Mirouze
- UMR5096, Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France.,UMR232, Diversité, Adaptation et Développement des Plantes, IRD, Montpellier, France.,UMR232, Diversité, Adaptation et Développement des Plantes, Université de Montpellier, Montpellier, France
| | | | - Melanie Pham
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Jin Hee Shin
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Corporate R&D, LG Chem, Seoul, Republic of Korea
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | | | | | - Nathan T Weeks
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agricultural Research Service, Ames, IA, USA
| | - Xinyou Zhang
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Oil Crops in Huanghuaihai Plains, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Zheng Zheng
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Oil Crops in Huanghuaihai Plains, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Ziqi Sun
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Oil Crops in Huanghuaihai Plains, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Lutz Froenicke
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Erez L Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | | | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Corley Holbrook
- Crop Genetics and Breeding Research Unit, US Department of Agriculture Agricultural Research Service, Tifton, GA, USA
| | | | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, US Department of Agriculture Agricultural Research Service, Stoneville, MS, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.,Department of Horticulture, University of Georgia, Tifton, GA, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agricultural Research Service, Ames, IA, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA. .,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA. .,Department of Crop and Soil Science, University of Georgia, Athens, GA, USA.
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA. .,Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
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10
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Wang L, Zhou X, Ren X, Huang L, Luo H, Chen Y, Chen W, Liu N, Liao B, Lei Y, Yan L, Shen J, Jiang H. A Major and Stable QTL for Bacterial Wilt Resistance on Chromosome B02 Identified Using a High-Density SNP-Based Genetic Linkage Map in Cultivated Peanut Yuanza 9102 Derived Population. Front Genet 2018; 9:652. [PMID: 30619474 PMCID: PMC6305283 DOI: 10.3389/fgene.2018.00652] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/30/2018] [Indexed: 11/29/2022] Open
Abstract
Bacterial wilt (BW) is one of the important diseases limiting the production of peanut (Arachis hypogaea L.) worldwide. The sufficient precise information on the quantitative trait loci (QTL) for BW resistance is essential for facilitating gene mining and applying in molecular breeding. Cultivar Yuanza 9102 is BW resistant, bred from wide cross between cultivated peanut Baisha 1016 and a wild diploid peanut species A. chacoense with BW resistance. In this study, we aim to map the major QTLs related to BW-resistance in Yuanza 9102. A high density SNP-based genetic linkage map was constructed through double-digest restriction-site-associated DNA sequencing (ddRADseq) technique based on Yuanza 9102 derived recombinant inbred lines (RILs) population. The map contained 2,187 SNP markers distributed on 20 linkage groups (LGs) spanning 1566.10 cM, and showed good synteny with AA genome from A. duranensis and BB genome from A. ipaensis. Phenotypic frequencies of BW resistance among RIL population showed two-peak distribution in four environments. Four QTLs explaining 5.49 to 23.22% phenotypic variance were identified to be all located on chromosome B02. The major QTL, qBWB02.1 (12.17–23.33% phenotypic variation explained), was detected in three environments showing consistent and stable expression. Furthermore, there was positive additive effect among these major and minor QTLs. The major QTL region was mapped to a region covering 2.3 Mb of the pseudomolecule B02 of A. ipaensis which resides in 21 nucleotide-binding site -leucine-rich repeat (NBS-LRR) encoding genes. The result of the major stable QTL (qBWB02.1) not only offers good foundation for discovery of BW resistant gene but also provide opportunity for deployment of the QTL in marker-assisted breeding in peanut.
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Affiliation(s)
- Lifang Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jinxiong Shen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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11
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Ren L, Huang W, Cannon EKS, Bertioli DJ, Cannon SB. A Mechanism for Genome Size Reduction Following Genomic Rearrangements. Front Genet 2018; 9:454. [PMID: 30356760 PMCID: PMC6189423 DOI: 10.3389/fgene.2018.00454] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
The factors behind genome size evolution have been of great interest, considering that eukaryotic genomes vary in size by more than three orders of magnitude. Using a model of two wild peanut relatives, Arachis duranensis and Arachis ipaensis, in which one genome experienced large rearrangements, we find that the main determinant in genome size reduction is a set of inversions that occurred in A. duranensis, and subsequent net sequence removal in the inverted regions. We observe a general pattern in which sequence is lost more rapidly at newly distal (telomeric) regions than it is gained at newly proximal (pericentromeric) regions - resulting in net sequence loss in the inverted regions. The major driver of this process is recombination, determined by the chromosomal location. Any type of genomic rearrangement that exposes proximal regions to higher recombination rates can cause genome size reduction by this mechanism. In comparisons between A. duranensis and A. ipaensis, we find that the inversions all occurred in A. duranensis. Sequence loss in those regions was primarily due to removal of transposable elements. Illegitimate recombination is likely the major mechanism responsible for the sequence removal, rather than unequal intrastrand recombination. We also measure the relative rate of genome size reduction in these two Arachis diploids. We also test our model in other plant species and find that it applies in all cases examined, suggesting our model is widely applicable.
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Affiliation(s)
- Longhui Ren
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, United States
| | - Wei Huang
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, United States.,Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Ethalinda K S Cannon
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, United States.,Department of Computer Science, Iowa State University, Ames, IA, United States
| | - David J Bertioli
- Institute of Biological Sciences, University of Brasiìlia, Brasiìlia, Brazil.,Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Ames, IA, United States
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12
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Chopra R, Simpson CE, Hillhouse A, Payton P, Sharma J, Burow MD. SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species. Mol Genet Genomics 2018; 293:1477-1491. [PMID: 30069598 DOI: 10.1007/s00438-018-1472-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/09/2018] [Indexed: 12/19/2022]
Abstract
KEY MESSAGE QTL mapping of important architectural traits was successfully applied to an A-genome diploid population using gene-specific variations. Peanut wild species are an important source of resistance to biotic and possibly abiotic stress; because these species differ from the cultigen in many traits, we have undertaken to identify QTLs for several plant architecture-related traits. In this study, we took recently identified SNPs, converted them into markers, and identified QTLs for architectural traits. SNPs from RNASeq data distinguishing two parents, A. duranensis (KSSc38901) and A. cardenasii (GKP10017), of a mapping population were identified using three references-A. duranensis V14167 genome sequence, and transcriptome sequences of A. duranensis KSSc38901 and OLin. More than 49,000 SNPs differentiated the parents, and 87.9% of the 190 SNP calls tested were validated. SNPs were then genotyped on 91 F2 lines using KASP chemistry on a Roche LightCycler 480 and a Fluidigm Biomark HD, and using SNPType chemistry on the Fluidigm Biomark HD. A linkage map was constructed having ten linkage groups, with 144 loci spanning a total map distance of 1040 cM. Comparison of the A-genome map to the A. duranensis genome sequence revealed a high degree of synteny. QTL analysis was also performed on the mapping population for important architectural traits. Fifteen definitive and 16 putative QTLs for petiole length, leaflet length and width, leaflet area, leaflet length/width ratio, main stem height, presence of flowers on the main stem, and seed mass were identified. Results demonstrate that SNPs identified from transcriptome sequencing could be converted to KASP or SNPType markers with a high success rate, and used to identify alleles with significant phenotypic effects, These could serve as information useful for introgression of alleles into cultivated peanut from wild species and have the potential to allow breeders to more easily fix these alleles using a marker-assisted backcrossing approach.
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Affiliation(s)
- Ratan Chopra
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | | | - Andrew Hillhouse
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA
| | | | - Jyotsna Sharma
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Mark D Burow
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
- Texas A&M AgriLife Research, Lubbock, TX, 79403, USA.
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13
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Varshney RK, Thudi M, Pandey MK, Tardieu F, Ojiewo C, Vadez V, Whitbread AM, Siddique KHM, Nguyen HT, Carberry PS, Bergvinson D. Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3293-3312. [PMID: 29514298 DOI: 10.1093/jxb/ery088] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/22/2018] [Indexed: 05/23/2023]
Abstract
Grain legumes form an important component of the human diet, provide feed for livestock, and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress, posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the past half century. To achieve faster genetic gains in legumes in rainfed conditions, this review proposes the integration of modern genomics approaches, high throughput phenomics, and simulation modelling in support of crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval, and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experimental plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains, including not only productivity but also nutritional and market traits, will increase the profitability of farming and the availability of affordable nutritious food especially in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Francois Tardieu
- French National Institute for Agricultural Research (INRA), Monpellier, France
| | - Chris Ojiewo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Institut de recherche pour le développement (IRD), Montpellier, France
| | - Anthony M Whitbread
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Peter S Carberry
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - David Bergvinson
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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14
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Leal-Bertioli SCM, Godoy IJ, Santos JF, Doyle JJ, Guimarães PM, Abernathy BL, Jackson SA, Moretzsohn MC, Bertioli DJ. Segmental allopolyploidy in action: Increasing diversity through polyploid hybridization and homoeologous recombination. AMERICAN JOURNAL OF BOTANY 2018; 105:1053-1066. [PMID: 29985538 DOI: 10.1002/ajb2.1112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/18/2018] [Indexed: 05/05/2023]
Abstract
PREMISE OF THE STUDY The genetic bottleneck of polyploid formation can be mitigated by multiple origins, gene flow, and recombination among different lineages. In crop plants with limited origins, efforts to increase genetic diversity have limitations. Here we used lineage recombination to increase genetic diversity in peanut, an allotetraploid likely of single origin, by crossing with a novel allopolyploid genotype and selecting improved lines. METHODS Single backcross progeny from cultivated peanut × wild species-derived allotetraploid cross were studied over successive generations. Using genetic assumptions that encompass segmental allotetraploidy, we used single nucleotide polymorphisms and whole-genome sequence data to infer genome structures. KEY RESULTS Selected lines, despite a high proportion of wild alleles, are agronomically adapted, productive, and with improved disease resistances. Wild alleles mostly substituted homologous segments of the peanut genome. Regions of dispersed wild alleles, characteristic of gene conversion, also occurred. However, wild chromosome segments sometimes replaced cultivated peanut's homeologous subgenome; A. ipaënsis B sometimes replaced A. hypogaea A subgenome (~0.6%), and A. duranensis replaced A. hypogaea B subgenome segments (~2%). Furthermore, some subgenome regions historically lost in cultivated peanut were "recovered" by wild chromosome segments (effectively reversing the "polyploid ratchet"). These processes resulted in lines with new genome structure variations. CONCLUSIONS Genetic diversity was introduced by wild allele introgression, and by introducing new genome structure variations. These results highlight the special possibilities of segmental allotetraploidy and of using lineage recombination to increase genetic diversity in peanut, likely mirroring what occurs in natural segmental allopolyploids with multiple origins.
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Affiliation(s)
- Soraya C M Leal-Bertioli
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Ignácio J Godoy
- Campinas Agronomical Institute, Avenida Barão de Itapura, 1.481, Campinas, SP, 13020-902, Brazil
| | - João F Santos
- Campinas Agronomical Institute, Avenida Barão de Itapura, 1.481, Campinas, SP, 13020-902, Brazil
| | - Jeff J Doyle
- Cornell University, School of Integrative Plant Science, Plant Breeding & Genetics Section, Ithaca, NY, 14853, USA
| | - Patrícia M Guimarães
- Embrapa Genetic Resources and Biotechnology, PqEB, W5 Norte Final, Brasília, DF, 70770-917, Brazil
| | - Brian L Abernathy
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Scott A Jackson
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA, 30602-6810, USA
| | - Márcio C Moretzsohn
- Embrapa Genetic Resources and Biotechnology, PqEB, W5 Norte Final, Brasília, DF, 70770-917, Brazil
| | - David J Bertioli
- University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA, 30602-6810, USA
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15
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Wang Z, Huai D, Zhang Z, Cheng K, Kang Y, Wan L, Yan L, Jiang H, Lei Y, Liao B. Development of a High-Density Genetic Map Based on Specific Length Amplified Fragment Sequencing and Its Application in Quantitative Trait Loci Analysis for Yield-Related Traits in Cultivated Peanut. FRONTIERS IN PLANT SCIENCE 2018; 9:827. [PMID: 29997635 PMCID: PMC6028809 DOI: 10.3389/fpls.2018.00827] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/28/2018] [Indexed: 05/20/2023]
Abstract
High-density genetic maps (HDGMs) are very useful for genomic studies and quantitative trait loci (QTL) mapping. However, the low frequency of DNA polymorphisms in peanut has limited the quantity of available markers and hindered the construction of a HDGM. This study generated a peanut genetic map with the highest number of high-quality SNPs based on specific locus amplified fragment sequencing (SLAF-seq) technology and a newly constructed RIL population ("ZH16" × "sd-H1"). The constructed HDGM included 3,630 SNP markers belonging to 2,636 bins on 20 linkage groups (LGs), and it covers 2,098.14 cM in length, with an average marker distance of 0.58 cM. This HDGM was applied for the following collinear comparison, scaffold anchoring and analysis of genomic characterization including recombination rates and segregation distortion in peanut. For QTL mapping of investigated 14 yield-related traits, a total of 62 QTLs were detected on 12 chromosomes across 3 environments, and the co-localization of QTLs was observed for these traits which were significantly correlated on phenotype. Two stable co-located QTLs for seed- and pod-related traits were significantly identified in the chromosomal end of B06 and B07, respectively. The construction of HDGM and QTL analysis for yield-related traits in this study provide useful information for fine mapping and functional analysis of genes as well as molecular marker-assisted breeding.
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16
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Classical and Molecular Approaches for Mapping of Genes and Quantitative Trait Loci in Peanut. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-63935-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
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17
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Clevenger J, Chu Y, Chavarro C, Agarwal G, Bertioli DJ, Leal-Bertioli SCM, Pandey MK, Vaughn J, Abernathy B, Barkley NA, Hovav R, Burow M, Nayak SN, Chitikineni A, Isleib TG, Holbrook CC, Jackson SA, Varshney RK, Ozias-Akins P. Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut. MOLECULAR PLANT 2017; 10:309-322. [PMID: 27993622 PMCID: PMC5315502 DOI: 10.1016/j.molp.2016.11.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/07/2016] [Accepted: 11/21/2016] [Indexed: 05/19/2023]
Abstract
Peanut (Arachis hypogaea; 2n = 4x = 40) is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facilitate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide polymorphisms (SNPs) were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic regions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone positive selection. These observations provide key insights on the inclusion of new genetic diversity in cultivated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.
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Affiliation(s)
- Josh Clevenger
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA
| | - Gaurav Agarwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - David J Bertioli
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA; University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, 70910-900 Brasília, DF, Brazil
| | - Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA; Embrapa Genetic Resources and Biotechnology, 70770-917 Brasília, DF, Brazil
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Justin Vaughn
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA
| | - Brian Abernathy
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA
| | | | - Ran Hovav
- Agricultural Research Organization, Plant Sciences Institute, 7528809 Rishon LeZion, Israel
| | - Mark Burow
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409-2122, USA
| | - Spurthi N Nayak
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Thomas G Isleib
- Department of Crop and Soil Sciences, North Carolina State University, Box 7629, Raleigh, NC 28695-7629, USA
| | | | - Scott A Jackson
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, Athens, GA 30602, USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, The University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA.
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18
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19
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Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability. G3-GENES GENOMES GENETICS 2016; 6:3825-3836. [PMID: 27729436 PMCID: PMC5144954 DOI: 10.1534/g3.115.026898] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.
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Zhou X, Xia Y, Liao J, Liu K, Li Q, Dong Y, Ren X, Chen Y, Huang L, Liao B, Lei Y, Yan L, Jiang H. Quantitative Trait Locus Analysis of Late Leaf Spot Resistance and Plant-Type-Related Traits in Cultivated Peanut (Arachis hypogaea L.) under Multi-Environments. PLoS One 2016; 11:e0166873. [PMID: 27870916 PMCID: PMC5117734 DOI: 10.1371/journal.pone.0166873] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/04/2016] [Indexed: 11/18/2022] Open
Abstract
Late leaf spot (LLS) is one of the most serious foliar diseases affecting peanut worldwide leading to huge yield loss. To understand the genetic basis of LLS and assist breeding in the future, we conducted quantitative trait locus (QTL) analysis for LLS and three plant-type-related traits including height of main stem (HMS), length of the longest branch (LLB) and total number of branches (TNB). Significant negative correlations were observed between LLS and the plant-type-related traits in multi-environments of a RIL population from the cross Zhonghua 5 and ICGV 86699. A total of 20 QTLs were identified for LLS, of which two QTLs were identified in multi-environments and six QTLs with phenotypic variation explained (PVE) more than 10%. Ten, seven, fifteen QTLs were identified for HMS, LLB and TNB, respectively. Of these, one, one, two consensus QTLs and three, two, three major QTLs were detected for HMS, LLB and TNB, respectively. Of all 52 unconditional QTLs for LLS and plant-type-related traits, 10 QTLs were clustered in five genetic regions, of which three clusters including five robust major QTLs overlapped between LLS and one of the plant-type-related traits, providing evidence that the correlation could be genetically constrained. On the other hand, conditional mapping revealed different numbers and different extent of additive effects of QTLs for LLS conditioned on three plant-type-related traits (HMS, LLB and TNB), which improved our understanding of interrelationship between LLS and plant-type-related traits at the QTL level. Furthermore, two QTLs, qLLSB6-7 and qLLSB1 for LLS resistance, were identified residing in two clusters of NB-LRR—encoding genes. This study not only provided new favorable QTLs for fine-mapping, but also suggested that the relationship between LLS and plant-type-related traits of HMS, LLB and TNB should be considered while breeding for improved LLS resistance in peanut.
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Affiliation(s)
- Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Youlin Xia
- Nanchong Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Junhua Liao
- Nanchong Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qiang Li
- Department of Plant Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yang Dong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- * E-mail:
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Tseng YC, Tillman BL, Peng Z, Wang J. Identification of major QTLs underlying tomato spotted wilt virus resistance in peanut cultivar Florida-EP(TM) '113'. BMC Genet 2016; 17:128. [PMID: 27600750 PMCID: PMC5012072 DOI: 10.1186/s12863-016-0435-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/25/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Spotted wilt caused by tomato spotted wilt virus (TSWV) is one of the major peanut (Arachis hypogaea L.) diseases in the southeastern United States. Occurrence, severity, and symptoms of spotted wilt disease are highly variable from season to season, making it difficult to efficiently evaluate breeding populations for resistance. Molecular markers linked to spotted wilt resistance could overcome this problem and allow selection of resistant lines regardless of environmental conditions. Florida-EP(TM) '113' is a spotted wilt resistant cultivar with a significantly lower infection frequency. However, the genetic basis is still unknown. The objective of this study is to map the major quantitative trait loci (QTLs) linked to spotted wilt resistance in Florida-EP(TM) '113'. RESULTS Among 2,431 SSR markers located across the whole peanut genome screened between the two parental lines, 329 were polymorphic. Those polymorphic markers were used to further genotype a representative set of individuals in a segregating population. Only polymorphic markers on chromosome A01 showed co-segregation between genotype and phenotype. Genotyping by sequencing (GBS) of the representative set of individuals in the segregating population also depicted a strong association between several SNPs on chromosome A01 and the trait, indicating a major QTL on chromosome A01. Therefore marker density was enriched on the A01 chromosome. A linkage map with 23 makers on chromosome A01 was constructed, showing collinearity with the physical map. Combined with phenotypic data, a major QTL flanked by marker AHGS4584 and GM672 was identified on chromosome A01, with up to 22.7 % PVE and 9.0 LOD value. CONCLUSION A major QTL controlling the spotted wilt resistance in Florida-EP(TM) '113' was identified. The resistance is most likely contributed by PI 576638, a hirsuta botanical-type line, introduced from Mexico with spotted wilt resistance. The flanking markers of this QTL can be used for further fine mapping and marker assisted selection in peanut breeding programs.
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Affiliation(s)
- Yu-Chien Tseng
- Agronomy Department, University of Florida, 2033 Mowry Road, Room 337 Cancer/Genetics Research Complex, Gainesville, FL 32610 USA
- North Florida Research and Education Center, University of Florida, Marianna, FL 32446 USA
| | - Barry L. Tillman
- Agronomy Department, University of Florida, 2033 Mowry Road, Room 337 Cancer/Genetics Research Complex, Gainesville, FL 32610 USA
- North Florida Research and Education Center, University of Florida, Marianna, FL 32446 USA
| | - Ze Peng
- Agronomy Department, University of Florida, 2033 Mowry Road, Room 337 Cancer/Genetics Research Complex, Gainesville, FL 32610 USA
| | - Jianping Wang
- Agronomy Department, University of Florida, 2033 Mowry Road, Room 337 Cancer/Genetics Research Complex, Gainesville, FL 32610 USA
- Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610 USA
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Zhou X, Dong Y, Zhao J, Huang L, Ren X, Chen Y, Huang S, Liao B, Lei Y, Yan L, Jiang H. Genomic survey sequencing for development and validation of single-locus SSR markers in peanut (Arachis hypogaea L.). BMC Genomics 2016; 17:420. [PMID: 27251557 PMCID: PMC4888616 DOI: 10.1186/s12864-016-2743-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/14/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single-locus markers have many advantages compared with multi-locus markers in genetic and breeding studies because their alleles can be assigned to particular genomic loci in diversity analyses. However, there is little research on single-locus SSR markers in peanut. Through the de novo assembly of DNA sequencing reads of A. hypogaea, we developed single-locus SSR markers in a genomic survey for better application in genetic and breeding studies of peanut. RESULTS In this study, DNA libraries with four different insert sizes were used for sequencing with 150 bp paired-end reads. Approximately 237 gigabases of clean data containing 1,675,631,984 reads were obtained after filtering. These reads were assembled into 2,102,446 contigs with an N50 length of 1,782 bp, and the contigs were further assembled into 1,176,527 scaffolds with an N50 of 3,920 bp. The total length of the assembled scaffold sequences was 2.0 Gbp, and 134,652 single-locus SSRs were identified from 375,180 SSRs. Among these developed single-locus SSRs, trinucleotide motifs were the most abundant, followed by tetra-, di-, mono-, penta- and hexanucleotide motifs. The most common motif repeats for the various types of single-locus SSRs have a tendency to be A/T rich. A total of 1,790 developed in silico single-locus SSR markers were chosen and used in PCR experiments to confirm amplification patterns. Of them, 1,637 markers that produced single amplicons in twelve inbred lines were considered putative single-locus markers, and 290 (17.7 %) showed polymorphisms. A further F2 population study showed that the segregation ratios of the 97 developed SSR markers, which showed polymorphisms between the parents, were consistent with the Mendelian inheritance law for single loci (1:2:1). Finally, 89 markers were assigned to an A. hypogaea linkage map. A subset of 100 single-locus SSR markers was shown to be highly stable and universal in a collection of 96 peanut accessions. A neighbor-joining tree of this natural population showed that genotypes have obviously correlation with botanical varieties. CONCLUSIONS We have shown that the detection of single-locus SSR markers from a de novo genomic assembly of a combination of different-insert-size libraries is highly efficient. This is the first report of the development of genome-wide single-locus markers for A. hypogaea, and the markers developed in this study will be useful for gene tagging, sequence scaffold assignment, linkage map construction, diversity analysis, variety identification and association mapping in peanut.
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Affiliation(s)
- Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yang Dong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Jiaojiao Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Shunmou Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.,Databridge Technologies Corporation, Wuhan, 430062, Hubei, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
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Song H, Wang P, Lin JY, Zhao C, Bi Y, Wang X. Genome-Wide Identification and Characterization of WRKY Gene Family in Peanut. FRONTIERS IN PLANT SCIENCE 2016; 7:534. [PMID: 27200012 PMCID: PMC4845656 DOI: 10.3389/fpls.2016.00534] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/04/2016] [Indexed: 05/18/2023]
Abstract
WRKY, an important transcription factor family, is widely distributed in the plant kingdom. Many reports focused on analysis of phylogenetic relationship and biological function of WRKY protein at the whole genome level in different plant species. However, little is known about WRKY proteins in the genome of Arachis species and their response to salicylic acid (SA) and jasmonic acid (JA) treatment. In this study, we identified 77 and 75 WRKY proteins from the two wild ancestral diploid genomes of cultivated tetraploid peanut, Arachis duranensis and Arachis ipaënsis, using bioinformatics approaches. Most peanut WRKY coding genes were located on A. duranensis chromosome A6 and A. ipaënsis chromosome B3, while the least number of WRKY genes was found in chromosome 9. The WRKY orthologous gene pairs in A. duranensis and A. ipaënsis chromosomes were highly syntenic. Our analysis indicated that segmental duplication events played a major role in AdWRKY and AiWRKY genes, and strong purifying selection was observed in gene duplication pairs. Furthermore, we translate the knowledge gained from the genome-wide analysis result of wild ancestral peanut to cultivated peanut to reveal that gene activities of specific cultivated peanut WRKY gene were changed due to SA and JA treatment. Peanut WRKY7, 8 and 13 genes were down-regulated, whereas WRKY1 and 12 genes were up-regulated with SA and JA treatment. These results could provide valuable information for peanut improvement.
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Affiliation(s)
- Hui Song
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
| | - Pengfei Wang
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
| | - Jer-Young Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Chuanzhi Zhao
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
| | - Yuping Bi
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
| | - Xingjun Wang
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
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The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 2016; 48:438-46. [PMID: 26901068 DOI: 10.1038/ng.3517] [Citation(s) in RCA: 457] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/29/2016] [Indexed: 12/20/2022]
Abstract
Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
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Leal-Bertioli SCM, Moretzsohn MC, Roberts PA, Ballén-Taborda C, Borba TCO, Valdisser PA, Vianello RP, Araújo ACG, Guimarães PM, Bertioli DJ. Genetic Mapping of Resistance to Meloidogyne arenaria in Arachis stenosperma: A New Source of Nematode Resistance for Peanut. G3 (BETHESDA, MD.) 2015; 6:377-90. [PMID: 26656152 PMCID: PMC4751557 DOI: 10.1534/g3.115.023044] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/30/2015] [Indexed: 11/27/2022]
Abstract
Root-knot nematodes (RKN; Meloidogyne sp.) are a major threat to crops in tropical and subtropical regions worldwide. The use of resistant crop varieties is the preferred method of control because nematicides are expensive, and hazardous to humans and the environment. Peanut (Arachis hypogaea) is infected by four species of RKN, the most damaging being M. arenaria, and commercial cultivars rely on a single source of resistance. In this study, we genetically characterize RKN resistance of the wild Arachis species A. stenosperma using a population of 93 recombinant inbred lines developed from a cross between A. duranensis and A. stenosperma. Four quantitative trait loci (QTL) located on linkage groups 02, 04, and 09 strongly influenced nematode root galling and egg production. Drought-related, domestication and agronomically relevant traits were also evaluated, revealing several QTL. Using the newly available Arachis genome sequence, easy-to-use KASP (kompetitive allele specific PCR) markers linked to the newly identified RKN resistance loci were developed and validated in a tetraploid context. Therefore, we consider that A. stenosperma has high potential as a new source of RKN resistance in peanut breeding programs.
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Affiliation(s)
- Soraya C M Leal-Bertioli
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF, 70770-917, Brazil Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602-6810
| | - Márcio C Moretzsohn
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF, 70770-917, Brazil
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, California 92521
| | | | - Tereza C O Borba
- Embrapa Rice and Beans, Rodovia GO-462, km 12 Zona Rural C.P. 179, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | - Paula A Valdisser
- Embrapa Rice and Beans, Rodovia GO-462, km 12 Zona Rural C.P. 179, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | - Rosana P Vianello
- Embrapa Rice and Beans, Rodovia GO-462, km 12 Zona Rural C.P. 179, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | - Ana Cláudia G Araújo
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF, 70770-917, Brazil
| | - Patricia M Guimarães
- Embrapa Genetic Resources and Biotechnology, PqEB W5 Norte Final, Brasília, DF, 70770-917, Brazil
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602-6810 University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
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Peng Z, Gallo M, Tillman BL, Rowland D, Wang J. Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut (Arachis hypogaea L.). Mol Genet Genomics 2015; 291:363-81. [PMID: 26362763 DOI: 10.1007/s00438-015-1115-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
Abstract
Molecular markers are important tools for genotyping in genetic studies and molecular breeding. The SSR and SNP are two commonly used marker systems developed from genomic or transcript sequences. The objectives of this study were to: (1) assemble and annotate the publicly available ESTs in Arachis and the in-house short reads, (2) develop and validate SSR and SNP markers, and (3) investigate the genetic diversity and population structure of the peanut breeding lines and the U.S. peanut mini core collection using developed SSR markers. An NCBI EST dataset with 252,951 sequences and an in-house 454 RNAseq dataset with 288,701 sequences were assembled separately after trimming. Transcript sequence comparison and phylogenetic analysis suggested that peanut is closer to cowpea and scarlet bean than to soybean, common bean and Medicago. From these two datasets, 6455 novel SSRs and 11,902 SNPs were identified. Of the discovered SSRs, 380 representing various SSR types were selected for PCR validation. The amplification rate was 89.2 %. Twenty-two (6.5 %) SSRs were polymorphic between at least one pair of four genotypes. Sanger sequencing of PCR products targeting 110 SNPs revealed 13 true SNPs between tetraploid genotypes and 193 homoeologous SNPs within genotypes. Eight out of the 22 polymorphic SSR markers were selected to evaluate the genetic diversity of Florida peanut breeding lines and the U.S. peanut mini core collection. This marker set demonstrated high discrimination power by displaying an average polymorphism information content value of 0.783, a combined probability of identity of 10(-11), and a combined power of exclusion of 0.99991. The structure analysis revealed four sub-populations among the peanut accessions and lines evaluated. The results of this study enriched the peanut genomic resources, provided over 6000 novel SSR markers and the credentials for true peanut SNP marker development, and demonstrated the power of newly developed SSR markers in genotyping peanut germplasm and breeding materials.
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Affiliation(s)
- Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Maria Gallo
- Molecular Biosciences and Bioengineering Department, University of Hawai'i-Mānoa, Honolulu, HI, 96822, USA
| | - Barry L Tillman
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Diane Rowland
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA. .,Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA.
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Bosamia TC, Mishra GP, Thankappan R, Dobaria JR. Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut. PLoS One 2015; 10:e0129127. [PMID: 26046991 PMCID: PMC4457858 DOI: 10.1371/journal.pone.0129127] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/04/2015] [Indexed: 11/18/2022] Open
Abstract
With the aim to increase the number of functional markers in resource poor crop like cultivated peanut (Arachis hypogaea), large numbers of available expressed sequence tags (ESTs) in the public databases, were employed for the development of novel EST derived simple sequence repeat (SSR) markers. From 16424 unigenes, 2784 (16.95%) SSRs containing unigenes having 3373 SSR motifs were identified. Of these, 2027 (72.81%) sequences were annotated and 4124 gene ontology terms were assigned. Among different SSR motif-classes, tri-nucleotide repeats (33.86%) were the most abundant followed by di-nucleotide repeats (27.51%) while AG/CT (20.7%) and AAG/CTT (13.25%) were the most abundant repeat-motifs. A total of 2456 EST-SSR novel primer pairs were designed, of which 366 unigenes having relevance to various stresses and other functions, were PCR validated using a set of 11 diverse peanut genotypes. Of these, 340 (92.62%) primer pairs yielded clear and scorable PCR products and 39 (10.66%) primer pairs exhibited polymorphisms. Overall, the number of alleles per marker ranged from 1-12 with an average of 3.77 and the PIC ranged from 0.028 to 0.375 with an average of 0.325. The identified EST-SSRs not only enriched the existing molecular markers kitty, but would also facilitate the targeted research in marker-trait association for various stresses, inter-specific studies and genetic diversity analysis in peanut.
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Affiliation(s)
- Tejas C. Bosamia
- Crop Improvement Division, ICAR- Directorate of Groundnut Research, Junagadh, Gujarat, 362001, India
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, Gujarat, 362001,India
| | - Gyan P. Mishra
- Crop Improvement Division, ICAR- Directorate of Groundnut Research, Junagadh, Gujarat, 362001, India
| | - Radhakrishnan Thankappan
- Crop Improvement Division, ICAR- Directorate of Groundnut Research, Junagadh, Gujarat, 362001, India
| | - Jentilal R. Dobaria
- Crop Improvement Division, ICAR- Directorate of Groundnut Research, Junagadh, Gujarat, 362001, India
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Clevenger J, Chavarro C, Pearl SA, Ozias-Akins P, Jackson SA. Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations. MOLECULAR PLANT 2015; 8:831-46. [PMID: 25676455 DOI: 10.1016/j.molp.2015.02.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/21/2015] [Accepted: 02/01/2015] [Indexed: 05/23/2023]
Abstract
Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole-genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms (SNPs) have become popular tools for genetic mapping, discovery and application of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs (BWA-mem and Bowtie 2) and variant callers (SAMtools, GATK, and Freebayes). Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.
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Affiliation(s)
- Josh Clevenger
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793, USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Stephanie A Pearl
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793, USA.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.
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Kanyika BTN, Lungu D, Mweetwa AM, Kaimoyo E, Njung'e VM, Monyo ES, Siambi M, He G, Prakash CS, Zhao Y, de Villiers SM. Identification of groundnut (Arachis hypogaea) SSR markers suitable for multiple resistance traits QTL mapping in African germplasm. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2014.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 2015; 199:1093-105. [PMID: 25701284 PMCID: PMC4391553 DOI: 10.1534/genetics.115.174607] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/14/2015] [Indexed: 11/18/2022] Open
Abstract
Arachis hypogaea L. (cultivated peanut) is an allotetraploid (2n = 4x = 40) with an AABB genome type. Based on cytogenetic studies it has been assumed that peanut and wild-derived induced AABB allotetraploids have classic allotetraploid genetic behavior with diploid-like disomic recombination only between homologous chromosomes, at the exclusion of recombination between homeologous chromosomes. Using this assumption, numerous linkage map and quantitative trait loci studies have been carried out. Here, with a systematic analysis of genotyping and gene expression data, we show that this assumption is not entirely valid. In fact, autotetraploid-like tetrasomic recombination is surprisingly frequent in recombinant inbred lines generated from a cross of cultivated peanut and an induced allotetraploid derived from peanut’s most probable ancestral species. We suggest that a better, more predictive genetic model for peanut is that of a “segmental allotetraploid” with partly disomic, partly tetrasomic genetic behavior. This intermediate genetic behavior has probably had a previously overseen, but significant, impact on the genome and genetics of cultivated peanut.
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Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L. Mol Genet Genomics 2015; 290:1169-80. [PMID: 25663138 DOI: 10.1007/s00438-014-0976-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022]
Abstract
Single-nucleotide polymorphisms, which can be identified in the thousands or millions from comparisons of transcriptome or genome sequences, are ideally suited for making high-resolution genetic maps, investigating population evolutionary history, and discovering marker-trait linkages. Despite significant results from their use in human genetics, progress in identification and use in plants, and particularly polyploid plants, has lagged. As part of a long-term project to identify and use SNPs suitable for these purposes in cultivated peanut, which is tetraploid, we generated transcriptome sequences of four peanut cultivars, namely OLin, New Mexico Valencia C, Tamrun OL07 and Jupiter, which represent the four major market classes of peanut grown in the world, and which are important economically to the US southwest peanut growing region. CopyDNA libraries of each genotype were used to generate 2 × 54 paired-end reads using an Illumina GAIIx sequencer. Raw reads were mapped to a custom reference consisting of Tifrunner 454 sequences plus peanut ESTs in GenBank, compromising 43,108 contigs; 263,840 SNP and indel variants were identified among four genotypes compared to the reference. A subset of 6 variants was assayed across 24 genotypes representing four market types using KASP chemistry to assess the criteria for SNP selection. Results demonstrated that transcriptome sequencing can identify SNPs usable as selectable DNA-based markers in complex polyploid species such as peanut. Criteria for effective use of SNPs as markers are discussed in this context.
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Hong Y, Pandey MK, Liu Y, Chen X, Liu H, Varshney RK, Liang X, Huang S. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis. FRONTIERS IN PLANT SCIENCE 2015; 6:1068. [PMID: 26697032 PMCID: PMC4667090 DOI: 10.3389/fpls.2015.01068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 11/16/2015] [Indexed: 05/06/2023]
Abstract
The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.
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Affiliation(s)
- Yanbin Hong
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Manish K. Pandey
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Ying Liu
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoping Chen
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hong Liu
- College of Agriculture, South China Agricultural UniversityGuangzhou, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
| | - Xuanqiang Liang
- Peanut Research Center, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shangzhi Huang
- School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
- *Correspondence: Shangzhi Huang
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Liu L, Dang PM, Chen CY. Development and Utilization of InDel Markers to Identify Peanut (Arachis hypogaea) Disease Resistance. FRONTIERS IN PLANT SCIENCE 2015; 6:988. [PMID: 26617627 PMCID: PMC4643128 DOI: 10.3389/fpls.2015.00988] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/29/2015] [Indexed: 05/04/2023]
Abstract
Peanut diseases, such as leaf spot and spotted wilt caused by Tomato Spotted Wilt Virus, can significantly reduce yield and quality. Application of marker assisted plant breeding requires the development and validation of different types of DNA molecular markers. Nearly 10,000 SSR-based molecular markers have been identified by various research groups around the world, but less than 14.5% showed polymorphism in peanut and only 6.4% have been mapped. Low levels of polymorphism limit the application of marker assisted selection (MAS) in peanut breeding programs. Insertion/deletion (InDel) markers have been reported to be more polymorphic than SSRs in some crops. The goals of this study were to identify novel InDel markers and to evaluate the potential use in peanut breeding. Forty-eight InDel markers were developed from conserved sequences of functional genes and tested in a diverse panel of 118 accessions covering six botanical types of cultivated peanut, of which 104 were from the U.S. mini-core. Results showed that 16 InDel markers were polymorphic with polymorphic information content (PIC) among InDels ranged from 0.017 to 0.660. With respect to botanical types, PICs varied from 0.176 for fastigiata var., 0.181 for hypogaea var., 0.306 for vulgaris var., 0.534 for aequatoriana var., 0.556 for peruviana var., to 0.660 for hirsuta var., implying that aequatoriana var., peruviana var., and hirsuta var. have higher genetic diversity than the other types and provide a basis for gene functional studies. Single marker analysis was conducted to associate specific marker to disease resistant traits. Five InDels from functional genes were identified to be significantly correlated to tomato spotted wilt virus (TSWV) infection and leaf spot, and these novel markers will be utilized to identify disease resistant genotype in breeding populations.
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Affiliation(s)
- Lifeng Liu
- Department of Crop, Soil and Environmental Sciences, Auburn UniversityAuburn, AL, USA
- Department of Agronomy, Agricultural University of HebeiBaoding, China
| | - Phat M. Dang
- National Peanut Research Laboratory, United States Department of Agriculture-Agricultural Research ServiceDawson, GA, USA
| | - Charles Y. Chen
- Department of Crop, Soil and Environmental Sciences, Auburn UniversityAuburn, AL, USA
- *Correspondence: Charles Y. Chen
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Chopra R, Burow G, Farmer A, Mudge J, Simpson CE, Burow MD. Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data. PLoS One 2014; 9:e115055. [PMID: 25551607 PMCID: PMC4281230 DOI: 10.1371/journal.pone.0115055] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/28/2014] [Indexed: 12/17/2022] Open
Abstract
The narrow genetic base and limited genetic information on Arachis species have hindered the process of marker-assisted selection of peanut cultivars. However, recent developments in sequencing technologies have expanded opportunities to exploit genetic resources, and at lower cost. To use the genetic information for Arachis species available at the transcriptome level, it is important to have a good quality reference transcriptome. The available Tifrunner 454 FLEX transcriptome sequences have an assembly with 37,000 contigs and low N50 values of 500-751bp. Therefore, we generated de novo transcriptome assemblies, with about 38 million reads in the tetraploid cultivar OLin, and 16 million reads in each of the diploids, A. duranensis K38901 and A. ipaënsis KGBSPSc30076 using three different de novo assemblers, Trinity, SOAPdenovo-Trans and TransAByss. All these assemblers can use single kmer analysis, and the latter two also permit multiple kmer analysis. Assemblies generated for all three samples had N50 values ranging from 1278–1641 bp in Arachis hypogaea (AABB), 1401–1492 bp in Arachis duranensis (AA), and 1107–1342 bp in Arachis ipaënsis (BB). Comparison with legume ESTs and protein databases suggests that assemblies generated had more than 40% full length transcripts with good continuity. Also, on mapping the raw reads to each of the assemblies generated, Trinity had a high success rate in assembling sequences compared to both TransAByss and SOAPdenovo-Trans. De novo assembly of OLin had a greater number of contigs (67,098) and longer contig length (N50 = 1,641) compared to the Tifrunner TSA. Despite having shorter read length (2×50) than the Tifrunner 454FLEX TSA, de novo assembly of OLin proved superior in comparison. Assemblies generated to represent different genome combinations may serve as a valuable resource for the peanut research community.
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Affiliation(s)
- Ratan Chopra
- Texas Tech University, Department of Plant and Soil Sciences, Lubbock, TX, 79409, United States of America
| | - Gloria Burow
- USDA-ARS-CSRL, 3810 4 Street, Lubbock, TX, 79415, United States of America
| | - Andrew Farmer
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, United States of America
| | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, United States of America
| | - Charles E. Simpson
- Texas A&M AgriLife Research, 1229 N. U.S. Highway 281, Stephenville, TX, 76401, United States of America
| | - Mark D. Burow
- Texas Tech University, Department of Plant and Soil Sciences, Lubbock, TX, 79409, United States of America
- Texas A&M AgriLife Research, 1102 East FM 1294, Lubbock, TX, 79403, United States of America
- * E-mail:
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Zhou X, Xia Y, Ren X, Chen Y, Huang L, Huang S, Liao B, Lei Y, Yan L, Jiang H. Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genomics 2014; 15:351. [PMID: 24885639 PMCID: PMC4035077 DOI: 10.1186/1471-2164-15-351] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 04/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cultivated peanut, or groundnut (Arachis hypogaea L.), is an important oilseed crop with an allotetraploid genome (AABB, 2n=4x=40). In recent years, many efforts have been made to construct linkage maps in cultivated peanut, but almost all of these maps were constructed using low-throughput molecular markers, and most show a low density, directly influencing the value of their applications. With advances in next-generation sequencing (NGS) technology, the construction of high-density genetic maps has become more achievable in a cost-effective and rapid manner. The objective of this study was to establish a high-density single nucleotide polymorphism (SNP)-based genetic map for cultivated peanut by analyzing next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq) reads. RESULTS We constructed reduced representation libraries (RRLs) for two A. hypogaea lines and 166 of their recombinant inbred line (RIL) progenies using the ddRADseq technique. Approximately 175 gigabases of data containing 952,679,665 paired-end reads were obtained following Solexa sequencing. Mining this dataset, 53,257 SNPs were detected between the parents, of which 14,663 SNPs were also detected in the population, and 1,765 of the obtained polymorphic markers met the requirements for use in the construction of a genetic map. Among 50 randomly selected in silico SNPs, 47 were able to be successfully validated. One linkage map was constructed, which was comprised of 1,685 marker loci, including 1,621 SNPs and 64 simple sequence repeat (SSR) markers. The map displayed a distribution of the markers into 20 linkage groups (LGs A01-A10 and B01-B10), spanning a distance of 1,446.7 cM. The alignment of the LGs from this map was shown in comparison with a previously integrated consensus map from peanut. CONCLUSIONS This study showed that the ddRAD library combined with NGS allowed the rapid discovery of a large number of SNPs in the cultivated peanut. The first high density SNP-based linkage map for A. hypogaea was generated that can serve as a reference map for cultivated Arachis species and will be useful in genetic mapping. Our results contribute to the available molecular marker resources and to the assembly of a reference genome sequence for the peanut.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, People's Republic of China.
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Abstract
Single nucleotide polymorphic markers (SNPs) are attractive for use in genetic mapping and marker-assisted breeding because they can be scored in parallel assays at favorable costs. However, scoring SNP markers in polyploid plants like the peanut is problematic because of interfering signal generated from the DNA bases that are homeologous to those being assayed. The present study used a previously constructed 1536 GoldenGate SNP assay developed using SNPs identified between two A. duranensis accessions. In this study, the performance of this assay was tested on two RIL mapping populations, one diploid (A. duranensis × A. stenosperma) and one tetraploid [A. hypogaea cv. Runner IAC 886 × synthetic tetraploid (A. ipaënsis × A. duranensis)4×]. The scoring was performed using the software GenomeStudio version 2011.1. For the diploid, polymorphic markers provided excellent genotyping scores with default software parameters. In the tetraploid, as expected, most of the polymorphic markers provided signal intensity plots that were distorted compared to diploid patterns and that were incorrectly scored using default parameters. However, these scorings were easily corrected using the GenomeStudio software. The degree of distortion was highly variable. Of the polymorphic markers, approximately 10% showed no distortion at all behaving as expected for single-dose markers, and another 30% showed low distortion and could be considered high-quality. The genotyped markers were incorporated into diploid and tetraploid genetic maps of Arachis and, in the latter case, were located almost entirely on A genome linkage groups.
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Sharma S, Upadhyaya HD, Varshney RK, Gowda CLL. Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes. FRONTIERS IN PLANT SCIENCE 2013; 4:309. [PMID: 23970889 PMCID: PMC3747629 DOI: 10.3389/fpls.2013.00309] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/23/2013] [Indexed: 05/18/2023]
Abstract
The narrow genetic base of cultivars coupled with low utilization of genetic resources are the major factors limiting grain legume production and productivity globally. Exploitation of new and diverse sources of variation is needed for the genetic enhancement of grain legumes. Wild relatives with enhanced levels of resistance/tolerance to multiple stresses provide important sources of genetic diversity for crop improvement. However, their exploitation for cultivar improvement is limited by cross-incompatibility barriers and linkage drags. Pre-breeding provides a unique opportunity, through the introgression of desirable genes from wild germplasm into genetic backgrounds readily used by the breeders with minimum linkage drag, to overcome this. Pre-breeding activities using promising landraces, wild relatives, and popular cultivars have been initiated at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) to develop new gene pools in chickpea, pigeonpea, and groundnut with a high frequency of useful genes, wider adaptability, and a broad genetic base. The availability of molecular markers will greatly assist in reducing linkage drags and increasing the efficiency of introgression in pre-breeding programs.
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Affiliation(s)
- Shivali Sharma
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
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Stalker HT, Tallury SP, Ozias-Akins P, Bertioli D, Bertioli SCL. The Value of Diploid Peanut Relatives for Breeding and Genomics. ACTA ACUST UNITED AC 2013. [DOI: 10.3146/ps13-6.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
ABSTRACT
Collection, evaluation, and introgression research has been conducted with Arachis species for more than 60 years. Eighty species in the genus have been described and additional species will be named in the future. Extremely high levels of disease and insect resistances to immunity have been observed in many species of the genus as compared to the cultivated peanut, which makes them extremely important for crop improvement. Many thousands of interspecific hybrids have been produced in the genus, but introgression has been slow because of genomic incompatibilities and sterility of hybrids. Genomics research was initiated during the late 1980s to characterize species relationships and investigate more efficient methods to introgress genes from wild species to A. hypogaea. Relatively low density genetic maps have been created from inter- and intra-specific crosses, several of which have placed disease resistance genes into limited linkage groups. Of particular interest is associating molecular markers with traits of interest to enhance breeding for disease and insect resistances. Only recently have sufficiently large numbers of markers become available to effectively conduct marker assisted breeding in peanut. Future analyses of the diploid ancestors of the cultivated peanut, A. duranensis and A. ipaensis, will allow more detailed characterization of peanut genetics and the effects of Arachis species alleles on agronomic traits. Extensive efforts are being made to create populations for genomic analyses of peanut, and introgression of genes from wild to cultivated genotypes should become more efficient in the near future.
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Affiliation(s)
- H. T. Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
| | - S. P. Tallury
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
| | - P. Ozias-Akins
- Department of Horticulture, The University of Georgia, Tifton, GA, 31973
| | - D. Bertioli
- Department of Gentics and Morphology, University of Brasilia, Campus Darcy Ribeiro, Brasília, DF. Brazil
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Guo B, Pandey MK, He G, Zhang X, Liao B, Culbreath A, Varshney RK, Nwosu V, Wilson RF, Stalker HT. Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut. ACTA ACUST UNITED AC 2013. [DOI: 10.3146/ps13-03.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
ABSTRACT
The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.
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Affiliation(s)
- Baozhu Guo
- USDA- Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA 31793
| | - Manish K. Pandey
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Guohao He
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Boshou Liao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Victor Nwosu
- Plant Science Program, Global Chocolate Science & Technology, Mars Chocolate North America, Hackettstown, NJ 07840
| | - Richard F. Wilson
- Oilseeds & Bioscience Consulting, 5517 Hickory Leaf Drive, Raleigh, NC 27606
| | - H. Thomas Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
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Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SCM, Thudi M, Pandey MK, Rami JF, Foncéka D, Gowda MVC, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res 2013; 20:173-84. [PMID: 23315685 PMCID: PMC3628447 DOI: 10.1093/dnares/dss042] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/21/2012] [Indexed: 02/02/2023] Open
Abstract
The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)(4×), were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.
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Guo Y, Khanal S, Tang S, Bowers JE, Heesacker AF, Khalilian N, Nagy ED, Zhang D, Taylor CA, Stalker HT, Ozias-Akins P, Knapp SJ. Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut. BMC Genomics 2012; 13:608. [PMID: 23140574 PMCID: PMC3532320 DOI: 10.1186/1471-2164-13-608] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. RESULTS A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B-genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A- and B-genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution. CONCLUSIONS Our findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut.
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Affiliation(s)
- Yufang Guo
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
- Department of Horticulture, The University of Georgia, Tifton, GA, 31973, USA
| | - Sameer Khanal
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Shunxue Tang
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - John E Bowers
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Adam F Heesacker
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Nelly Khalilian
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Ervin D Nagy
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Dong Zhang
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - Christopher A Taylor
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
| | - H Thomas Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Peggy Ozias-Akins
- Department of Horticulture, The University of Georgia, Tifton, GA, 31973, USA
| | - Steven J Knapp
- Institute of Plant Breeding, Genetics, and Genomics, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA
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