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Tomlekova N, Idziak-Helmcke D, Franke P, Rojek-Jelonek M, Kwasniewska J. Phaseolus vulgaris mutants reveal variation in the nuclear genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1308830. [PMID: 38239224 PMCID: PMC10794375 DOI: 10.3389/fpls.2023.1308830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024]
Abstract
Phaseolus vulgaris L. (common bean) is an essential source of proteins in the human diet worldwide. Bean breeding programs to increase genetic diversity based on induced mutagenesis have a long tradition in Bulgaria. Common bean varieties with high productivity, wide environmental adaptability, good nutritional properties, and improved disease resistance have been successfully developed. In this study, we aimed to investigate selected nuclear genome features, such as the genome size, the number and chromosomal distribution of 5S and 35S rDNA loci by using the fluorescence in situ hybridization (FISH), as well as the level of DNA damage in some local Bulgarian accessions and mutants of P. vulgaris. Flow cytometry analyses revealed no significant differences in genome size between analyzed lines except for one of the analyzed mutants, M19. The value of genome size 2C DNA is about 1.37 pg2C -1 for all lines, whereas it is 1.42 pg2C-1 for M19. The chromosome number remains the same (2n=22) for all analyzed lines. Results of FISH analyses showed that the number of 5S rDNA was stable among accessions and mutant lines (four loci), while the number of 35S rDNA loci was shown as highly polymorphic, varying between ten and sixteen, and displaying differences in the size and location of 35S rDNA loci between analyzed genotypes. The cell cycle profile was different for the analyzed genotypes. The results revealed that wide variation in genome organization and size as well as DNA damage characterizes the analyzed genetic resources of the common bean.
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Affiliation(s)
- Nasya Tomlekova
- Laboratory of Molecular Biology, Department of Breeding, Marisa Vegetable Crops Research Institute, Plovdiv, Agricultural Academy, Sofia, Bulgaria
| | - Dominika Idziak-Helmcke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paula Franke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Magdalena Rojek-Jelonek
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jolanta Kwasniewska
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Nawaz I, Zeb T, Ali GM, Zeb BS, Jalal A, Rehman MU, Bakht T, Ali S. High Genetic Diversity in the Himalayan Common Bean ( Phaseolus vulgaris) Germplasm with Divergence from Its Center of Origin in the Mesoamerica and Andes. ACS OMEGA 2023; 8:48787-48797. [PMID: 38162784 PMCID: PMC10753573 DOI: 10.1021/acsomega.3c05150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
The common bean is found in the Himalayan region of Pakistan with substantial morphological variability. Genetic diversity within any crop species is a precursor for genetic improvement; however, little is known about common bean genetic diversity in this region. We explored the genetic diversity in the common bean from the Himalayan region (Khyber Pakhtunkhwa, Gilgit-Baltistan, Kashmir) of Pakistan. Microsatellite genotyping was carried out for 147 samples with 40 simple sequence repeat (SSR) markers. The results revealed a clear divergence of the Pakistani population from the primary gene pool (with FST values of 0.2 with Andes and 0.27 with Mesoamerica). However, within the Himalayan germplasm, no clear evidence of spatial structure was observed (with the maximum FST values of only 0.025), probably due to the dispersal of seeds by human activity within the region. This was further elucidated by the discriminant analyses of principal components. Considering the diversity parameters, high genotypic diversity was observed for the indigenous lines (0.990), comparable to the primary gene pool (0.976 for Mesoamerica and 0.976 for Andes populations). A high genotypic diversity was observed within the Himalayan population (ranging from 0.500 for Upper Dir to 0.952 for Mansehra). Gene diversity across loci varied between 0.28 for Chitral to 0.38 for Kurram. Our results suggested a divergent and independent evolution of the Himalayan population, which might have led to the diversification of the common bean germplasm in the region postintroduction into the region. The diversity observed could also be exploited in future breeding programs for the development and introduction of climate-resilient varieties.
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Affiliation(s)
- Iffat Nawaz
- The
University of Agriculture Peshawar, Peshawar 25130, Khyber Pakhtunkhwa, Pakistan
| | - Tehseen Zeb
- The
University of Agriculture Peshawar, Peshawar 25130, Khyber Pakhtunkhwa, Pakistan
| | | | - Bibi Saima Zeb
- The
University of Agriculture Peshawar, Peshawar 25130, Khyber Pakhtunkhwa, Pakistan
| | - Abdullah Jalal
- The
University of Agriculture Peshawar, Peshawar 25130, Khyber Pakhtunkhwa, Pakistan
| | - Monsif Ur Rehman
- Department
of Agriculture, Hazara University, Mansehra, Mansehra 21120, Pakistan
| | - Tamana Bakht
- Shaheed
Benazir Bhutto university Sheringal Dir upper, Dir Upper 18200, Pakistan
| | - Sajid Ali
- Department
of Agriculture, Hazara University, Mansehra, Mansehra 21120, Pakistan
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Kumar K, Gupta P, Singh KN, Nirgude MS, Srivastava H, Sharma S, Sevanthi AM, Durgesh K, Jain PK, Gaikwad K. Whole chloroplast genome-specific non-synonymous SNPs reveal the presence of substantial diversity in the pigeonpea mini-core collection. 3 Biotech 2023; 13:365. [PMID: 37840876 PMCID: PMC10575842 DOI: 10.1007/s13205-023-03785-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D ( - 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03785-8.
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Affiliation(s)
- Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh India
| | - Palak Gupta
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Kumar Durgesh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
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Nina N, Theoduloz C, Paillán H, Jiménez-Aspee F, Márquez K, Schuster K, Becker L, Oellig C, Frank J, Schmeda-Hirschmann G. Chemical profile and bioactivity of Chilean bean landraces (Phaseolus vulgaris L.). J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
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Yatsenko VV. Breeding value of non-shooting forms of winter garlic in the conditions of the Right Bank Forest-Steppe of Ukraine. PLANT VARIETIES STUDYING AND PROTECTION 2022. [DOI: 10.21498/2518-1017.18.3.2022.268999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Purpose. To investigate the degree of reduced scape of softneck collection specimens of winter garlic of different ecological and geographical origin in the conditions of the Right Bank Forest-Steppe of Ukraine. Methods. During 2020–2022, nine local and introduced varieties of winter garlic (Nos. 19, 27, 33, 43 and 44 from Cherkasy) were studied in field conditions (Uman, 48°46’N, 30°14’E) region, No. 14 from Ternopil region, No. 1 from Spain, No. 16 from France and No. 35 from Azerbaijan). Generally accepted methods of genetico-statistical analysis were used to evaluate the garlic collection. Results. The research revealed that the weight of the bulb decreased by 7.6–31.1%, depending on the sample, and the yield by 6.1–38.6% during the formation of a reduced scape. Among the collection samples, according to the “bulb weight” indicator, Nos. 16 and 44 stood out – 57.22 and 52.24 g, respectively, of the sample. Adaptable for this feature were samples Nos. 16, 19 and 44; intensive – Nos. 16, 27, 33 and 44, and stable samples were Nos. 14, 19, 35 and 43. A significant relationship between the coefficient of genetic and environmental variation (CVG/CVA) for the traits “bulb weight” and “yield” was revealed. However, CVG/CVA ratio ≥ 1 is required to obtain high performance. Samples were selected as the initial material for further breeding based on the “yield” feature: according to adaptability and ecological plasticity – Nos. 16 and 44; according to stability – Nos. 19, 35 and 43 and samples of the intensive type – 16, 27, 33 and 44, which will ensure high yields in optimal cultivation conditions. All studied samples that formed air bulbs were characterized by a very large 1000 bulb weight, on average 1156.76 g. The maximum of 1000 bulb weight was characteristic for samples No. 16 and 27 – 1225.73 and 1638.0 g, respectively. Conclusions. The data obtained in the Right Bank Forest-Steppe of Ukraine will be used to develop a breeding research scheme under the conditions of introduction. As a result of the research, a working collection of raw material was created for the breeding of garlic by the classical method – clonal breeding.
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Rodriguez DFC, Urban MO, Santaella M, Gereda JM, Contreras AD, Wenzl P. Using phenomics to identify and integrate traits of interest for better-performing common beans: A validation study on an interspecific hybrid and its Acutifolii parents. FRONTIERS IN PLANT SCIENCE 2022; 13:1008666. [PMID: 36570940 PMCID: PMC9773562 DOI: 10.3389/fpls.2022.1008666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Evaluations of interspecific hybrids are limited, as classical genebank accession descriptors are semi-subjective, have qualitative traits and show complications when evaluating intermediate accessions. However, descriptors can be quantified using recognized phenomic traits. This digitalization can identify phenomic traits which correspond to the percentage of parental descriptors remaining expressed/visible/measurable in the particular interspecific hybrid. In this study, a line of P. vulgaris, P. acutifolius and P. parvifolius accessions and their crosses were sown in the mesh house according to CIAT seed regeneration procedures. METHODOLOGY Three accessions and one derived breeding line originating from their interspecific crosses were characterized and classified by selected phenomic descriptors using multivariate and machine learning techniques. The phenomic proportions of the interspecific hybrid (line INB 47) with respect to its three parent accessions were determined using a random forest and a respective confusion matrix. RESULTS The seed and pod morphometric traits, physiological behavior and yield performance were evaluated. In the classification of the accession, the phenomic descriptors with highest prediction force were Fm', Fo', Fs', LTD, Chl, seed area, seed height, seed Major, seed MinFeret, seed Minor, pod AR, pod Feret, pod round, pod solidity, pod area, pod major, pod seed weight and pod weight. Physiological traits measured in the interspecific hybrid present 2.2% similarity with the P. acutifolius and 1% with the P. parvifolius accessions. In addition, in seed morphometric characteristics, the hybrid showed 4.5% similarity with the P. acutifolius accession. CONCLUSIONS Here we were able to determine the phenomic proportions of individual parents in their interspecific hybrid accession. After some careful generalization the methodology can be used to: i) verify trait-of-interest transfer from P. acutifolius and P. parvifolius accessions into their hybrids; ii) confirm selected traits as "phenomic markers" which would allow conserving desired physiological traits of exotic parental accessions, without losing key seed characteristics from elite common bean accessions; and iii) propose a quantitative tool that helps genebank curators and breeders to make better-informed decisions based on quantitative analysis.
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Affiliation(s)
- Diego Felipe Conejo Rodriguez
- Genetic Resources Program, International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira, Valle del Cauca, Colombia
| | - Milan Oldřich Urban
- Bean Physiology and Breeding Program, International Center for Tropical Agriculture, Recta Cali-Palmira, Valle del Cauca, Colombia
| | - Marcela Santaella
- Genetic Resources Program, International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira, Valle del Cauca, Colombia
| | - Javier Mauricio Gereda
- Genetic Resources Program, International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira, Valle del Cauca, Colombia
| | - Aquiles Darghan Contreras
- Department of Agronomy, Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Peter Wenzl
- Genetic Resources Program, International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira, Valle del Cauca, Colombia
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Islam NS, Duwadi K, Chen L, Pajak A, McDowell T, Marsolais F, Dhaubhadel S. Global analysis of common bean multidrug and toxic compound extrusion transporters (PvMATEs): PvMATE8 and pinto bean seed coat darkening. FRONTIERS IN PLANT SCIENCE 2022; 13:1046597. [PMID: 36438155 PMCID: PMC9686396 DOI: 10.3389/fpls.2022.1046597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
In common bean (Phaseolus vulgaris L.), postharvest seed coat darkening is an undesirable trait that affects crop value. The increased accumulation of proanthocyanidins (PAs) in the seed coat results in darker seeds in many market classes of colored beans after harvest. The precursors of PAs are synthesized in the cytoplasm, and subsequently get glycosylated and then transported to the vacuoles where polymerization occurs. Thus, vacuolar transporters play an important role in the accumulation of PAs. Here, we report that common bean genome contains 59 multidrug and toxic compound extrusion genes (PvMATEs). Phylogenetic analysis of putative PvMATEs with functionally characterized MATEs from other plant species categorized them into substrate-specific clades. Our data demonstrate that a vacuolar transporter PvMATE8 is expressed at a higher level in the pinto bean cultivar CDC Pintium (regular darkening) compared to 1533-15 (slow darkening). PvMATE8 localizes in the vacuolar membrane and rescues the PA deficient (tt12) mutant phenotype in Arabidopsis thaliana. Analysis of PA monomers in transgenic seeds together with wild-type and mutants suggests a possible feedback regulation of PA biosynthesis and accumulation. Identification of PvMATE8 will help better understand the mechanism of PA accumulation in common bean.
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Affiliation(s)
- Nishat S. Islam
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kishor Duwadi
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ling Chen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Aga Pajak
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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Plant conservation in the Mesoamerican biodiversity hotspot: a case study on the Piper genus in Veracruz (Mexico). Trop Ecol 2022. [DOI: 10.1007/s42965-022-00271-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Giordani W, Gama HC, Chiorato AF, Marques JPR, Huo H, Benchimol-Reis LL, Camargo LEA, Garcia AAF, Vieira MLC. Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection. THE PLANT GENOME 2022; 15:e20161. [PMID: 34806826 DOI: 10.1002/tpg2.20161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crops. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging because little has been done to discover resistance genes or markers to assist selection. We performed genome-wide association studies and quantitative trait loci mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and the root-galling index were evaluated. Complex genetic architecture and independent genomic regions were associated with each trait. Single nucleotide polymorphisms on chromosomes Pv06, Pv07, Pv08, and Pv11 were associated with the number of egg masses, and SNPs on Pv01, Pv02, Pv05, and Pv10 were associated with root-galling. A total of 216 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA sequencing analysis. Histochemical analysis indicated that reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance, and the candidate genes are valuable targets for functional investigation and gene editing approaches.
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Affiliation(s)
- Willian Giordani
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - Henrique Castro Gama
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | | | | | - Heqiang Huo
- Mid-Florida Research and Education Center, Univ. of Florida, Apopka, FL, 32703, USA
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Suárez JC, Contreras AT, Anzola JA, Vanegas JI, Rao IM. Physiological Characteristics of Cultivated Tepary Bean (Phaseolus acutifolius A. Gray) and Its Wild Relatives Grown at High Temperature and Acid Soil Stress Conditions in the Amazon Region of Colombia. PLANTS 2021; 11:plants11010116. [PMID: 35009119 PMCID: PMC8747739 DOI: 10.3390/plants11010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/12/2021] [Accepted: 12/18/2021] [Indexed: 11/30/2022]
Abstract
Common bean (Phaseolus vulgaris L.) is sensitive to different types of abiotic stresses (drought, high temperature, low soil fertility, and acid soil), and this may limit its adaptation and consequently to its yield under stress. Because of this, a sister species, tepary bean (Phaseolus acutifolius A. Gray), has recently gained attention in breeding for improved abiotic stress tolerance in common bean. In this study, we evaluated the adaptation of 302 accessions of tepary bean (Phaseolus acutifolius A. Gray) and its wild relatives (grouped in four types of tepary bean genetic resource: cultivated, acutifolius regressive, acutifolius wild, tenuifolius wild) when grown under high temperature and acid soil conditions with aluminum toxicity in the Amazon region of Colombia. Our objective was to determine differences among four types of tepary bean genetic resource in their morpho-phenological, agronomic, and physiological responses to combined high temperature and acid soil stress conditions. We found that cultivated P. acutifolius var acutifolius presented a greater number of pods per plant, as well as larger seeds and a greater number of seeds per pod. Some traits, such as root biomass, days to flowering and physiological maturity, specific leaf area, and stomatal density, showed significant differences between types of tepary bean genetic resource, probably contributing to difference in adaptation to combined stress conditions of high temperature and acid soil conditions. The photochemical quenching (qP) was higher in cultivated P. acutifolius var. acutifolius, while energy dissipation by non-photochemical quenching (NPQ) in the form of heat and the coefficient of non-photochemical dissipation (qN) were higher in acutifolius regressive and tenuifolius wild accessions. We have identified 6 accessions of cultivated and 19 accessions of tenuifolius wild that exhibited grain yields above 1800 kg ha−1. These accessions could be suitable to use as parents to improve dry seed production of tepary bean under combined stress conditions of high temperature and acid soil.
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Affiliation(s)
- Juan Carlos Suárez
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia; (A.T.C.); (J.A.A.); (J.I.V.)
- Programa de Maestría en Sistemas Sostenibles de Producción, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia
- Grupo de Investigaciones Agroecosistemas y Conservación en Bosques Amazónicos-GAIA, Centro de Investigaciones Amazónicas CIMAZ Macagual César Augusto Estrada González, Florencia 180001, Colombia
- Correspondence: ; Tel.: +57-320-280-4455
| | - Amara Tatiana Contreras
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia; (A.T.C.); (J.A.A.); (J.I.V.)
- Programa de Maestría en Sistemas Sostenibles de Producción, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia
| | - José Alexander Anzola
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia; (A.T.C.); (J.A.A.); (J.I.V.)
| | - José Iván Vanegas
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia; (A.T.C.); (J.A.A.); (J.I.V.)
| | - Idupulapati M. Rao
- International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Cali 763537, Colombia;
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Lugo-Morin DR. Building an Ethnic Food Ethic: The Case of the Ngigua Indigenous People of Southern Puebla, Mexico. ACTA ACUST UNITED AC 2021; 7:3. [PMID: 34746372 PMCID: PMC8557708 DOI: 10.1007/s41055-021-00095-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 11/27/2022]
Abstract
Food ethics in the indigenous context is associated with a historical and profound relationship that indigenous groups have with nature. To address this relationship and identify the food uses associated with the maguey plant from a biocultural perspective among the Ngigua indigenous people living in the municipality of Tlacotepec de Benito Juárez in Puebla, the three main communities in the municipality of Tlacotepec de Benito Juárez that make use of the maguey plant were chosen. The study was carried out with a qualitative approach, using a semi-structured interview as a research technique. The analysis carried out recognises the importance of the maguey plant as a biocultural resource for the Ngigua in a context of ethical deliberation. Among the food uses associated with the maguey plant, the following are identified: pulque (a drink of pre-Hispanic origin) and red worm. Women play an important role, participating in 80% of the preparation of both foods. The cultural environment of the maguey is a way of life that, in the case of the Ngigua people, represents a strategic element for survival. In times of food crisis, the study shows how ethnic food strategies in a context of ethical deliberation can constitute an alternative for the design of food solutions in territories with food shortages.
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Affiliation(s)
- Diosey Ramon Lugo-Morin
- Postgraduate Program in Sustainable Management of Natural Resources, Management of Socioecological Systems, Research and Postgraduate Studies, Intercultural University of Puebla State, Huehuetla, Mexico
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12
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Wang S, Guo C, Xing Z, Li M, Yang H, Zhang Y, Ren F, Chen L, Mi S. Dietary Intervention With α-Amylase Inhibitor in White Kidney Beans Added Yogurt Modulated Gut Microbiota to Adjust Blood Glucose in Mice. Front Nutr 2021; 8:664976. [PMID: 34712684 PMCID: PMC8545863 DOI: 10.3389/fnut.2021.664976] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
White kidney beans contain α-amylase inhibitors that can be used in diet for weight reduction. In this study, we investigated the potential of white kidney bean (phaseolus vulgaris L.) extract enriched in α-amylase inhibitor as a food additive in yogurt to regulate blood glucose in hyperglycemic animals. Five groups of C57BL/6J mice were fed for 8 weeks with standard chow diets, high-fat diets (HFD), or high-fat diets with supplement of α-amylase inhibitor in white kidney beans (P. vulgaris extract, PVE), yogurt (Y), and PVE added yogurt (YPVE), respectively. The HFD weakened glucose tolerance and caused insulin resistance in mice, and changed the characteristics of intestinal flora. The intervention of Y, PVE, and YPVE decreased blood glucose, insulin, hyperlipidemia, and inflammatory cytokine levels in mice fed with HFD. Moreover, the YPVE could regulate the components of host intestinal microbiota toward a healthy pattern, significantly increased the metabolic-related flora Corynebacterium, Granulicatella, and Streptococcus, while it decreased Paraprevotella and Allobaculum. Thus, YPVE markedly increased functions of "Amino Acid Metabolism," "Energy Metabolism," "Nucleotide Metabolism," and declined functions of "Glycan Biosynthesis and Metabolism." Consequently, YPVE could be developed as a new functional food because of its beneficial prebiotic properties in the metabolic syndrome.
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Affiliation(s)
- Shenli Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, China.,Brand Food R&D Center, Nutrition & Health Research Institute (China Oil & Foodstuffs Corporation-NHRI), Beijing, China
| | - Chongye Guo
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Zhikai Xing
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Meng Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Haiying Yang
- Brand Food R&D Center, Nutrition & Health Research Institute (China Oil & Foodstuffs Corporation-NHRI), Beijing, China
| | - Yunting Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fazheng Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, China
| | - Lishui Chen
- Brand Food R&D Center, Nutrition & Health Research Institute (China Oil & Foodstuffs Corporation-NHRI), Beijing, China
| | - Shuangli Mi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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13
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de Carvalho Paulino JF, de Almeida CP, Song Q, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans. J Appl Genet 2021; 62:585-600. [PMID: 34386968 DOI: 10.1007/s13353-021-00657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/15/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.
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Affiliation(s)
| | - Caléo Panhoca de Almeida
- Common Bean Genetic Group, Natural Center of Plant Genetics, Agronomic Institute (IAC), Campinas, SP, Brazil
| | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA-ARS, Beltsville, MD, USA
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Chacón-Sánchez MI, Martínez-Castillo J, Duitama J, Debouck DG. Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.618709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The genus Phaseolus, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus Phaseolus in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus Phaseolus from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several Phaseolus species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus Phaseolus since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.
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15
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Paulino JFDC, de Almeida CP, Bueno CJ, Song Q, Fritsche-Neto R, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean. Genes (Basel) 2021; 12:765. [PMID: 34069884 PMCID: PMC8157364 DOI: 10.3390/genes12050765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 12/31/2022] Open
Abstract
Fusarium wilt (Fusarium oxysporum f. sp. phaseoli, Fop) is one of the main fungal soil diseases in common bean. The aim of the present study was to identify genomic regions associated with Fop resistance through genome-wide association studies (GWAS) in a Mesoamerican Diversity Panel (MDP) and to identify potential common bean sources of Fop's resistance. The MDP was genotyped with BARCBean6K_3BeadChip and evaluated for Fop resistance with two different monosporic strains using the root-dip method. Disease severity rating (DSR) and the area under the disease progress curve (AUDPC), at 21 days after inoculation (DAI), were used for GWAS performed with FarmCPU model. The p-value of each SNP was determined by resampling method and Bonferroni test. For UFV01 strain, two significant single nucleotide polymorphisms (SNPs) were mapped on the Pv05 and Pv11 for AUDPC, and the same SNP (ss715648096) on Pv11 was associated with AUDPC and DSR. Another SNP, mapped on Pv03, showed significance for DSR. Regarding IAC18001 strain, significant SNPs on Pv03, Pv04, Pv05, Pv07 and on Pv01, Pv05, and Pv10 were observed. Putative candidate genes related to nucleotide-binding sites and carboxy-terminal leucine-rich repeats were identified. The markers may be important future tools for genomic selection to Fop disease resistance in beans.
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Affiliation(s)
| | - Caléo Panhoca de Almeida
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas 13075-630, SP, Brazil; (J.F.d.C.P.); (C.P.d.A.)
| | - César Júnior Bueno
- Centro Avançado de Pesquisa em Proteção de Plantas e Saúde Animal, Instituto Biológico, Campinas 13101-680, SP, Brazil;
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA;
| | - Roberto Fritsche-Neto
- Department of Genetics, ‘Luiz de Queiroz’ Agriculture College, University of Sao Paulo, Piracicaba 13418-900, SP, Brazil;
| | | | - Alisson Fernando Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico, Campinas 13075-630, SP, Brazil; (S.A.M.C.); (A.F.C.)
| | - Luciana Lasry Benchimol-Reis
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas 13075-630, SP, Brazil; (J.F.d.C.P.); (C.P.d.A.)
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Ángel Martín-Rodríguez J, Ariani A, Leija A, Elizondo A, Fuentes SI, Ramirez M, Gepts P, Hernández G, Formey D. Phaseolus vulgaris MIR1511 genotypic variations differentially regulate plant tolerance to aluminum toxicity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1521-1533. [PMID: 33300202 DOI: 10.1111/tpj.15129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/20/2020] [Accepted: 12/03/2020] [Indexed: 05/28/2023]
Abstract
The common-bean (Phaseolus vulgaris), a widely consumed legume, originated in Mesoamerica and expanded to South America, resulting in the development of two geographically distinct gene pools. Poor soil condition, including metal toxicity, are often constraints to common-bean crop production. Several P. vulgaris miRNAs, including miR1511, respond to metal toxicity. The MIR1511 gene sequence from the two P. vulgaris model sequenced genotypes revealed that, as opposed to BAT93 (Mesoamerican), the G19833 (Andean) accession displays a 58-bp deletion, comprising the mature and star miR1511 sequences. Genotyping-By-Sequencing data analysis from 87 non-admixed Phaseolus genotypes, comprising different Phaseolus species and P. vulgaris populations, revealed that all the P. vulgaris Andean genotypes and part of the Mesoamerican (MW1) genotypes analyzed displayed a truncated MIR1511 gene. The geographic origin of genotypes with a complete versus truncated MIR1511 showed a distinct distribution. The P. vulgaris ALS3 (Aluminum Sensitive Protein 3) gene, known to be important for aluminum detoxification in several plants, was experimentally validated as the miR1511 target. Roots from BAT93 plants showed decreased miR1511 and increased ALS3 transcript levels at early stages under aluminum toxicity (AlT), while G19833 plants, lacking mature miR1511, showed higher and earlier ALS3 response. Root architecture analyses evidenced higher tolerance of G19833 plants to AlT. However, G19833 plants engineered for miR1511 overexpression showed lower ALS3 transcript level and increased sensitivity to AlT. Absence of miR1511 in Andean genotypes, resulting in a diminished ALS3 transcript degradation, appears to be an evolutionary advantage to high Al levels in soils with increased drought conditions.
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Affiliation(s)
| | - Andrea Ariani
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Armando Elizondo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara I Fuentes
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramirez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Larranaga N, van Zonneveld M, Hormaza JI. Holocene land and sea-trade routes explain complex patterns of pre-Columbian crop dispersion. THE NEW PHYTOLOGIST 2021; 229:1768-1781. [PMID: 33089900 DOI: 10.1111/nph.16936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/06/2020] [Indexed: 05/17/2023]
Abstract
Pre-Columbian crop movement remains poorly understood, hampering a good interpretation of the domestication and diversification of Neotropical crops. To provide new insights into pre-Columbian crop movement, we applied spatial genetics to identify and compare dispersal routes of three American crops between Mesoamerica and the Andes, two important centres of pre-Columbian crop and cultural diversity. Our analysis included georeferenced simple-sequence repeats (SSR) marker datasets of 1852 genotypes of cherimoya (Annona cherimola Mill.), a perennial fruit crop that became underutilised in the Americas after the European conquest, 770 genotypes of maize (Zea mays L.) and 476 genotypes of common bean (Phaseolus vulgaris L.). Our findings show that humans brought cherimoya from Mesoamerica to present Peru through long-distance sea-trade routes across the Pacific Ocean at least 4700 yr bp, after more ancient dispersion of maize and other crops through the Mesoamerican isthmus over land and near-coastal waters. To our knowledge, this is the first evidence of pre-Columbian crop movement between Mesoamerica and the Andes across the Pacific Ocean providing new insights into pre-Columbian crop exchange in the Americas. We propose that cherimoya represents a wider group of perennial fruit crops dispersed by humans via sea-trade routes between Mesoamerica and the Andes across the Pacific Ocean.
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Affiliation(s)
- Nerea Larranaga
- Instituto de Hortofruticultura Subtropical y Mediterranea La Mayora (IHSM La Mayora - CSIC - UMA), Algarrobo, 29750, Spain
- IMAREFI, University of Guadalajara, Jalisco, 45110, México
| | - Maarten van Zonneveld
- Genetic Resources and Seed Unit, World Vegetable Center, Shanhua, 74151, Taiwan
- Bioversity International, Turrialba, Costa Rica, 7170, Spain
| | - Jose I Hormaza
- Instituto de Hortofruticultura Subtropical y Mediterranea La Mayora (IHSM La Mayora - CSIC - UMA), Algarrobo, 29750, Spain
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Ramirez‐Villegas J, Khoury CK, Achicanoy HA, Mendez AC, Diaz MV, Sosa CC, Debouck DG, Kehel Z, Guarino L. A gap analysis modelling framework to prioritize collecting for ex situ conservation of crop landraces. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Julian Ramirez‐Villegas
- International Center for Tropical Agriculture (CIAT) Cali Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), c/o CIAT Cali Colombia
| | - Colin K. Khoury
- International Center for Tropical Agriculture (CIAT) Cali Colombia
- United States Department of Agriculture Agricultural Research Service National Laboratory for Genetic Resources Preservation Fort Collins CO USA
- Department of Biology Saint Louis University St. Louis MO USA
| | | | - Andres C. Mendez
- International Center for Tropical Agriculture (CIAT) Cali Colombia
| | | | | | | | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA) Rabat Morocco
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Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces. DIVERSITY 2019. [DOI: 10.3390/d11090154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.
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20
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Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. MICROBIOME 2019; 7:114. [PMID: 31412927 PMCID: PMC6694607 DOI: 10.1186/s40168-019-0727-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. RESULTS Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. CONCLUSIONS Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.
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Affiliation(s)
- Juan E. Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
| | - Camilo A. Ramírez
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Rodrigo Mendes
- Embrapa Meio Ambiente, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000 Brazil
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
| | - Víctor J. Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
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21
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Wilker J, Navabi A, Rajcan I, Marsolais F, Hill B, Torkamaneh D, Pauls KP. Agronomic Performance and Nitrogen Fixation of Heirloom and Conventional Dry Bean Varieties Under Low-Nitrogen Field Conditions. FRONTIERS IN PLANT SCIENCE 2019; 10:952. [PMID: 31404343 PMCID: PMC6676800 DOI: 10.3389/fpls.2019.00952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/09/2019] [Indexed: 05/26/2023]
Abstract
Common beans (Phaseolus vulgaris) form a relationship with nitrogen-fixing rhizobia and through a process termed symbiotic nitrogen fixation (SNF) which provides them with a source of nitrogen. However, beans are considered poor nitrogen fixers, and modern production practices involve routine use of N fertilizer, which leads to the down-regulation of SNF. High-yielding, conventionally bred bean varieties are developed using conventional production practices and selection criteria, typically not including SNF efficiency, and may have lost this trait over decades of modern breeding. In contrast, heirloom bean genotypes were developed before the advent of modern production practices and may represent an underutilized pool of genetics which could be used to improve SNF. This study compared the SNF capacity under low-N field conditions, of collections of heirloom varieties with and conventionally bred dry bean varieties. The heirloom-conventional panel (HCP) consisted of 42 genotypes from various online seed retailers or from the University of Guelph Bean Breeding program seedbank. The HCP was genotyped using a single nucleotide polymorphism (SNP) array to investigate genetic relatedness within the panel. Field trials were conducted at three locations in ON, Canada from 2014 to 2015 and various agronomic and seed composition traits were measured, including capacity for nitrogen fixation (using the natural abundance method to measure seed N isotope ratios). Significant variation for SNF was found in the panel. However, on average, heirloom genotypes did not fix significantly more nitrogen than conventionally bred varieties. However, five heirloom genotypes fixed >60% of their nitrogen from the atmosphere. Yield (kg ha-1) was not significantly different between heirloom and conventional genotypes, suggesting that incorporating heirloom genotypes into a modern breeding program would not negatively impact yield. Nitrogen fixation was significantly higher among Middle American genotypes than among Andean genotypes, confirming previous findings. The best nitrogen fixing line was Coco Sophie, a European heirloom white bean whose genetic makeup is admixed between the Andean and Middle American genepools. Heirloom genotypes represent a useful source of genetics to improve SNF in modern bean breeding.
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Affiliation(s)
- Jennifer Wilker
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Brett Hill
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - K. Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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Genetic Diversity within Snap Beans and Their Relation to Dry Beans. Genes (Basel) 2018; 9:genes9120587. [PMID: 30487476 PMCID: PMC6315957 DOI: 10.3390/genes9120587] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 11/17/2022] Open
Abstract
Two hundred forty-six snap bean genotypes and 49 dry beans representing both centers of domestication and six bean races with materials from Europe, Asia, and the Americas were genotyped using a single nucleotide polymorphism (SNP) array. The data was analyzed for expected heterozygosity, K-means clustering, principal components, phylogenetic relationships, and population substructure. When all gene pools of snap bean were assembled, the expected heterozygosity was roughly equivalent to a carefully chosen panel of dry beans representing all bean races and centers of domestication demonstrating the genetic richness of snap materials in total. K-means clustering and K = 2 structure analysis showed significant mixing of gene pools in the European and American commercial snap materials and the dominance of the Andean center of domestication among commercial contemporary snap beans. Conversely, the same analysis showed that Chinese, Iberian, and heirloom materials were underrepresented in contemporary materials. Further, Structure analysis revealed eight distinct groups within snap beans. Two showed strong kinship to the Middle American center of domestication, three to the Andean center of domestication, and three showed admixture between the two centers. Snap beans may have been independently derived from dry beans more than once and from both centers. Overall, we identified eight potential germplasm pools for snap bean.
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23
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Campa A, Murube E, Ferreira JJ. Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing. Genes (Basel) 2018; 9:E518. [PMID: 30360561 PMCID: PMC6266623 DOI: 10.3390/genes9110518] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 11/16/2022] Open
Abstract
A common bean (Phaseolus vulgaris) diversity panel of 308 lines was established from local Spanish germplasm, as well as old and elite cultivars mainly used for snap consumption. Most of the landraces included derived from the Spanish common bean core collection, so this panel can be considered to be representative of the Spanish diversity for this species. The panel was characterized by 3099 single-nucleotide polymorphism markers obtained through genotyping-by-sequencing, which revealed a wide genetic diversity and a low level of redundant material within the panel. Structure, cluster, and principal component analyses revealed the presence of two main subpopulations corresponding to the two main gene pools identified in common bean, the Andean and Mesoamerican pools, although most lines (70%) were associated with the Andean gene pool. Lines showing recombination between the two gene pools were also observed, most of them showing useful for snap bean consumption, which suggests that both gene pools were probably used in the breeding of snap bean cultivars. The usefulness of this panel for genome-wide association studies was tested by conducting association mapping for determinacy. Significant marker⁻trait associations were found on chromosome Pv01, involving the gene Phvul.001G189200, which was identified as a candidate gene for determinacy in the common bean.
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Affiliation(s)
- Ana Campa
- Plant Genetics, Area of Horticultural and Forest Crops, SERIDA, 33300 Asturias, Spain.
| | - Ester Murube
- Plant Genetics, Area of Horticultural and Forest Crops, SERIDA, 33300 Asturias, Spain.
| | - Juan José Ferreira
- Plant Genetics, Area of Horticultural and Forest Crops, SERIDA, 33300 Asturias, Spain.
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Nadeem MA, Habyarimana E, Çiftçi V, Nawaz MA, Karaköy T, Comertpay G, Shahid MQ, Hatipoğlu R, Yeken MZ, Ali F, Ercişli S, Chung G, Baloch FS. Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information. PLoS One 2018; 13:e0205363. [PMID: 30308006 PMCID: PMC6181364 DOI: 10.1371/journal.pone.0205363] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/20/2018] [Indexed: 12/31/2022] Open
Abstract
Turkey presents a great diversity of common bean landraces in farmers' fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2-3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.
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Affiliation(s)
- Muhammad Azhar Nadeem
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Ephrem Habyarimana
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria–Centro di ricerca cerealicoltura e colture industriali, Bologna, Italy
| | - Vahdettin Çiftçi
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Tolga Karaköy
- Organic Agriculture Program, Vocational School of Sivas, University of Cumhuriyet, Sivas, Turkey
| | - Gonul Comertpay
- Eastern Mediterranean Agricultural Research Institute, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio resources, South China Agricultural University, Guangzhou, China
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Mehmet Zahit Yeken
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Fawad Ali
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Faheem Shehzad Baloch
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
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Singh J, Zhao J, Vallejos CE. Differential transcriptome patterns associated with early seedling development in a wild and a domesticated common bean (Phaseolus vulgaris L.) accession. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:153-162. [PMID: 30080599 DOI: 10.1016/j.plantsci.2018.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Genes that control "Domestication Syndrome" traits were direct targets of selection, like those controlling increased seed size in the common bean. However, selection for this trait brought about unintentional selection on genes controlling seedling growth. We hypothesized that wild and domesticated plants have different early seedling growth patterns as an indirect consequence of selection for a larger seed size during domestication, and those differences resulted from changes in gene expression patterns of the wild ancestor. Large seeds pose a challenge to reserve remobilization during early heterotrophic growth, particularly during a transition towards more fertile alluvial soils. To address our hypothesis, we characterized the patterns of gene expression of cotyledon, root, and leaf tissues of 7-day old seedlings of a wild and a landrace accession of the common bean. Differential expression analyses detected genes with contrasting patterns of expression between the two genotypes in all three tissues. Some of the differentially expressed genes with contrasting genotypic patterns are known to have domestication-related signatures of selection. Among these genes were some transcription factors associated with key roles in development. These genes may represent targets of indirect selection and ultimately explain the growth phenotypic differences between wild and domesticated seedlings.
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Affiliation(s)
- Jugpreet Singh
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Jianxin Zhao
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
| | - C Eduardo Vallejos
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
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Scaldaferro MA, Barboza GE, Acosta MC. Evolutionary history of the chili pepper Capsicum baccatum L. (Solanaceae): domestication in South America and natural diversification in the Seasonally Dry Tropical Forests. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Marisel A Scaldaferro
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Argentina
- Facultad de Ciencias Exactas, Físicas y Naturales (Universidad Nacional de Córdoba), Argentina
| | - Gloria E Barboza
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Argentina
- Facultad de Ciencias Químicas (Universidad Nacional de Córdoba), Argentina
| | - M Cristina Acosta
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Argentina
- Facultad de Ciencias Exactas, Físicas y Naturales (Universidad Nacional de Córdoba), Argentina
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27
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Nepal MP, Andersen EJ, Neupane S, Benson BV. Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. Genes (Basel) 2017; 8:E249. [PMID: 28973974 PMCID: PMC5664099 DOI: 10.3390/genes8100249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022] Open
Abstract
Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence.
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Affiliation(s)
- Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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Nordenstedt N, Marcenaro D, Chilagane D, Mwaipopo B, Rajamäki ML, Nchimbi-Msolla S, Njau PJR, Mbanzibwa DR, Valkonen JPT. Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania. PLoS One 2017; 12:e0178242. [PMID: 28542624 PMCID: PMC5444779 DOI: 10.1371/journal.pone.0178242] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 05/10/2017] [Indexed: 12/29/2022] Open
Abstract
Common bean (Phaseolus vulgaris) is an annual grain legume that was domesticated in Mesoamerica (Central America) and the Andes. It is currently grown widely also on other continents including Africa. We surveyed seedborne viruses in new common bean varieties introduced to Nicaragua (Central America) and in landraces and improved varieties grown in Tanzania (eastern Africa). Bean seeds, harvested from Nicaragua and Tanzania, were grown in insect-controlled greenhouse or screenhouse, respectively, to obtain leaf material for virus testing. Equal amounts of total RNA from different samples were pooled (30-36 samples per pool), and small RNAs were deep-sequenced (Illumina). Assembly of the reads (21-24 nt) to contiguous sequences and searches for homologous viral sequences in databases revealed Phaseolus vulgaris endornavirus 1 (PvEV-1) and PvEV-2 in the bean varieties in Nicaragua and Tanzania. These viruses are not known to cause symptoms in common bean and are considered non-pathogenic. The small-RNA reads from each pool of samples were mapped to the previously characterized complete PvEV-1 and PvEV-2 sequences (genome lengths ca. 14 kb and 15 kb, respectively). Coverage of the viral genomes was 87.9-99.9%, depending on the pool. Coverage per nucleotide ranged from 5 to 471, confirming virus identification. PvEV-1 and PvEV-2 are known to occur in Phaseolus spp. in Central America, but there is little previous information about their occurrence in Nicaragua, and no information about occurrence in Africa. Aside from Cowpea mild mosaic virus detected in bean plants grown from been seeds harvested from one region in Tanzania, no other pathogenic seedborne viruses were detected. The low incidence of infections caused by pathogenic viruses transmitted via bean seeds may be attributable to new, virus-resistant CB varieties released by breeding programs in Nicaragua and Tanzania.
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Affiliation(s)
- Noora Nordenstedt
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Delfia Marcenaro
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Nicaraguan Institute of Agricultural Technology (CNIAB-INTA), Managua, Nicaragua
| | - Daudi Chilagane
- Sokoine University of Agriculture, Morogoro, Tanzania
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - Beatrice Mwaipopo
- Sokoine University of Agriculture, Morogoro, Tanzania
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | | | | | | | | | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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Bitocchi E, Rau D, Bellucci E, Rodriguez M, Murgia ML, Gioia T, Santo D, Nanni L, Attene G, Papa R. Beans ( Phaseolus ssp.) as a Model for Understanding Crop Evolution. FRONTIERS IN PLANT SCIENCE 2017; 8:722. [PMID: 28533789 PMCID: PMC5420584 DOI: 10.3389/fpls.2017.00722] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/19/2017] [Indexed: 05/03/2023]
Abstract
Here, we aim to provide a comprehensive and up-to-date overview of the most significant outcomes in the literature regarding the origin of Phaseolus genus, the geographical distribution of the wild species, the domestication process, and the wide spread out of the centers of origin. Phaseolus can be considered as a unique model for the study of crop evolution, and in particular, for an understanding of the convergent phenotypic evolution that occurred under domestication. The almost unique situation that characterizes the Phaseolus genus is that five of its ∼70 species have been domesticated (i.e., Phaseolus vulgaris, P. coccineus, P. dumosus, P. acutifolius, and P. lunatus), and in addition, for P. vulgaris and P. lunatus, the wild forms are distributed in both Mesoamerica and South America, where at least two independent and isolated episodes of domestication occurred. Thus, at least seven independent domestication events occurred, which provides the possibility to unravel the genetic basis of the domestication process not only among species of the same genus, but also between gene pools within the same species. Along with this, other interesting features makes Phaseolus crops very useful in the study of evolution, including: (i) their recent divergence, and the high level of collinearity and synteny among their genomes; (ii) their different breeding systems and life history traits, from annual and autogamous, to perennial and allogamous; and (iii) their adaptation to different environments, not only in their centers of origin, but also out of the Americas, following their introduction and wide spread through different countries. In particular for P. vulgaris this resulted in the breaking of the spatial isolation of the Mesoamerican and Andean gene pools, which allowed spontaneous hybridization, thus increasing of the possibility of novel genotypes and phenotypes. This knowledge that is associated to the genetic resources that have been conserved ex situ and in situ represents a crucial tool in the hands of researchers, to preserve and evaluate this diversity, and at the same time, to identify the genetic basis of adaptation and to develop new improved varieties to tackle the challenges of climate change, and food security and sustainability.
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Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Domenico Rau
- Department of Agriculture, University of SassariSassari, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | | | - Maria L. Murgia
- Department of Agriculture, University of SassariSassari, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of BasilicataPotenza, Italy
| | - Debora Santo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
| | - Giovanna Attene
- Department of Agriculture, University of SassariSassari, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic UniversityAncona, Italy
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Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 2016; 17:134. [PMID: 27339192 PMCID: PMC4918201 DOI: 10.1186/s13059-016-1004-2] [Citation(s) in RCA: 716] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.
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Affiliation(s)
- Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA.
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming Yu
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, South 40th St, Philadelphia, PA, 19104-6030, USA
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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31
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Meegahakumbura MK, Wambulwa MC, Thapa KK, Li MM, Möller M, Xu JC, Yang JB, Liu BY, Ranjitkar S, Liu J, Li DZ, Gao LM. Indications for Three Independent Domestication Events for the Tea Plant (Camellia sinensis (L.) O. Kuntze) and New Insights into the Origin of Tea Germplasm in China and India Revealed by Nuclear Microsatellites. PLoS One 2016; 11:e0155369. [PMID: 27218820 PMCID: PMC4878758 DOI: 10.1371/journal.pone.0155369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 04/27/2016] [Indexed: 11/18/2022] Open
Abstract
Background Tea is the world’s most popular non-alcoholic beverage. China and India are known to be the largest tea producing countries and recognized as the centers for the domestication of the tea plant (Camellia sinensis (L.) O. Kuntze). However, molecular studies on the origin, domestication and relationships of the main teas, China type, Assam type and Cambod type are lacking. Methodology/Principal Findings Twenty-three nuclear microsatellite markers were used to investigate the genetic diversity, relatedness, and domestication history of cultivated tea in both China and India. Based on a total of 392 samples, high levels of genetic diversity were observed for all tea types in both countries. The cultivars clustered into three distinct genetic groups (i.e. China tea, Chinese Assam tea and Indian Assam tea) based on STRUCTURE, PCoA and UPGMA analyses with significant pairwise genetic differentiation, corresponding well with their geographical distribution. A high proportion (30%) of the studied tea samples were shown to possess genetic admixtures of different tea types suggesting a hybrid origin for these samples, including the Cambod type. Conclusions We demonstrate that Chinese Assam tea is a distinct genetic lineage from Indian Assam tea, and that China tea sampled from India was likely introduced from China directly. Our results further indicate that China type tea, Chinese Assam type tea and Indian Assam type tea are likely the result of three independent domestication events from three separate regions across China and India. Our findings have important implications for the conservation of genetic stocks, as well as future breeding programs.
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Affiliation(s)
- M. K. Meegahakumbura
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- University of Chinese Academy of Science, Beijing 10049, China
- Coconut Research Institute, Lunuwila, Sri Lanka
| | - M. C. Wambulwa
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- University of Chinese Academy of Science, Beijing 10049, China
- World Agroforestry Centre, Nairobi, Kenya
| | - K. K. Thapa
- Department of Botany, Dinhata College, Dinhata– 736135, West Bengal, India
| | - M. M. Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- University of Chinese Academy of Science, Beijing 10049, China
| | - M. Möller
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, United Kingdom
| | - J. C. Xu
- Centre for Mountain Ecosystem Studies and World Agroforestry Centre East and Central Asia Regional Office, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
| | - J. B. Yang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
| | - B. Y. Liu
- Tea Research Institute of Yunnan Academy of Agricultural Sciences, Menghai 666201, China
| | - S. Ranjitkar
- Centre for Mountain Ecosystem Studies and World Agroforestry Centre East and Central Asia Regional Office, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
| | - J. Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
| | - D. Z. Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- University of Chinese Academy of Science, Beijing 10049, China
- * E-mail: (LMG); (DZL)
| | - L. M. Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
- * E-mail: (LMG); (DZL)
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Rodriguez M, Rau D, Bitocchi E, Bellucci E, Biagetti E, Carboni A, Gepts P, Nanni L, Papa R, Attene G. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris. THE NEW PHYTOLOGIST 2016; 209:1781-94. [PMID: 26526745 DOI: 10.1111/nph.13713] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/06/2015] [Indexed: 05/19/2023]
Abstract
Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources.
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Affiliation(s)
- Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Surigheddu, 07040, Alghero, Italy
| | - Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Eleonora Biagetti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Andrea Carboni
- Centro di Ricerca per le Colture Industriali (CRA-CIN), Consiglio per la Ricerca e la Sperimentazione in Agricoltura, via di Corticella, 133, 40128, Bologna, Italy
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Laura Nanni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. de Nicola, 07100, Sassari, Italy
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Surigheddu, 07040, Alghero, Italy
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Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol 2016; 17:32. [PMID: 26911872 PMCID: PMC4766624 DOI: 10.1186/s13059-016-0883-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/22/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. RESULTS We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. CONCLUSIONS The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.
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Affiliation(s)
- Anna Vlasova
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 LT, Utrecht, The Netherlands
| | - Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - André E Minoche
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW, 2010, Australia
| | - Ionas Erb
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Francisco Câmara
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Pablo Prieto-Barja
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - André Corvelo
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Walter Sanseverino
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Gastón Westergaard
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Juliane C Dohm
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Georgios J Pappas
- Department of Cellular Biology, University of Brasilia, Biological Science Institute, Brasília, DF, 70790-160, Brazil
| | - Soledad Saburido-Alvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Darek Kedra
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Irene Gonzalez
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Jessica Gómez-Garrido
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - María A Aguilar-Morón
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Nuria Andreu
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Maik Zehnsdorf
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Martín P Vázquez
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Alejandro Mentaberry
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA, Buenos Aires, Argentina
| | | | - José Luís García
- Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), 28040, Madrid, Spain
| | - Tyler Alioto
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Federico Sánchez
- Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain.
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Kenyon SG, Buerki S, Hansson C, Alvarez N, Benrey B. Uncovering Cryptic Parasitoid Diversity in Horismenus (Chalcidoidea, Eulophidae). PLoS One 2015; 10:e0136063. [PMID: 26352700 PMCID: PMC4564207 DOI: 10.1371/journal.pone.0136063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022] Open
Abstract
Horismenus parasitoids are an abundant and understudied group of eulophid wasps found mainly in the New World. Recent surveys based on morphological analyses in Costa Rica have quadrupled the number of named taxa, with more than 400 species described so far. This recent revision suggests that there is still a vast number of unknown species to be identified. As Horismenus wasps have been widely described as parasitoids of insect pests associated with crop plants, it is of high importance to properly establish the extant diversity of the genus, in order to provide biological control practitioners with an exhaustive catalog of putative control agents. In this study, we first collected Horismenus wasps from wild Phaseolus bean seeds in Central Mexico and Arizona to assess the genetic relatedness of three morphologically distinct species with overlapping host and geographical ranges. Sequence data from two nuclear and two mitochondrial gene regions uncovered three cryptic species within each of the three focal species (i.e., H. missouriensis, H. depressus and H. butcheri). The monophyly of each cryptic group is statistically supported (except in two of them represented by one single tip in which monophyly cannot be tested). The phylogenetic reconstruction is discussed with respect to differences between gene regions as well as likely reasons for the differences in variability between species.
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Affiliation(s)
- Sarah G. Kenyon
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchatel, Neuchâtel, Switzerland
| | - Sven Buerki
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, United Kingdom
| | - Christer Hansson
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, United Kingdom
- Museum of Biology (Entomology), Lund University, Lund, Sweden
| | - Nadir Alvarez
- Department of Ecology and Evolution, Biophore Dorigny, University of Lausanne, Lausanne, Switzerland
| | - Betty Benrey
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchatel, Neuchâtel, Switzerland
- * E-mail:
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Moyib OK, Alashiri GO, Adejoye OD. Chemometric dissimilarity in nutritive value of popularly consumed Nigerian brown and white common beans. Food Chem 2015; 166:576-584. [PMID: 25053096 DOI: 10.1016/j.foodchem.2014.06.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 06/15/2014] [Accepted: 06/16/2014] [Indexed: 11/26/2022]
Abstract
Brown beans are the preferred varieties over the white beans in Nigeria due to their assumed richer nutrients. This study was aimed at assessing and characterising some popular Nigerian common beans for their nutritive value based on seed coat colour. Three varieties, each, of Nigerian brown and white beans, and one, each, of French bean and soybean were analysed for 19 nutrients. Z-statistics test showed that Nigerian beans are nutritionally analogous to French bean and soybean. Analysis of variance showed that seed coat colour varied with proximate nutrients, Ca, Fe, and Vit C. Chemometric analysis methods revealed superior beans for macro and micro nutrients and presented clearer groupings among the beans for seed coat colour. The study estimated a moderate genetic distance (GD) that will facilitate transfer of useful genes and intercrossing among the beans. It also offers an opportunity to integrate French bean and soybean into genetic improvement programs in Nigerian common beans.
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Affiliation(s)
- Oluwasayo Kehinde Moyib
- Department of Chemical Sciences, Tai Solarin University of Education, Ijagun, PMB 2118 Ijebu-Ode, Nigeria.
| | | | - Oluseyi Damilola Adejoye
- Department of Biological Sciences, Tai Solarin University of Education, Ijagun, PMB 2118 Ijebu-Ode, Nigeria
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Blair MW, Córdoba JM, Muñóz C, Yuyó DK. BAC-end microsatellites from intra and inter-genic regions of the common bean genome and their correlation with cytogenetic features. PLoS One 2014; 9:e101873. [PMID: 25254501 PMCID: PMC4177843 DOI: 10.1371/journal.pone.0101873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 06/12/2014] [Indexed: 11/19/2022] Open
Abstract
Highly polymorphic markers such as simple sequence repeats (SSRs) or microsatellites are very useful for genetic mapping. In this study novel SSRs were identified in BAC-end sequences (BES) from non-contigged, non-overlapping bacterial artificial clones (BACs) in common bean (Phaseolus vulgaris L.). These so called "singleton" BACs were from the G19833 Andean gene pool physical map and the new BES-SSR markers were used for the saturation of the inter-gene pool, DOR364×G19833 genetic map. A total of 899 SSR loci were found among the singleton BES, but only 346 loci corresponded to the single di- or tri-nucleotide motifs that were likely to be polymorphic (ATT or AG motifs, principally) and useful for primer design and individual marker mapping. When these novel SSR markers were evaluated in the DOR364×G19833 population parents, 136 markers revealed polymorphism and 106 were mapped. Genetic mapping resulted in a map length of 2291 cM with an average distance between markers of 5.2 cM. The new genetic map was compared to the most recent cytogenetic analysis of common bean chromosomes. We found that the new singleton BES-SSR were helpful in filling peri-centromeric spaces on the cytogenetic map. Short genetic distances between some new singleton-derived BES-SSR markers was common showing suppressed recombination in these regions compared to other parts of the genome. The correlation of singleton-derived SSR marker distribution with other cytogenetic features of the bean genome is discussed.
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Affiliation(s)
- Matthew Wohlgemuth Blair
- Departamento de Agronomía y Ciencias Agricolas, Universidad Nacional de Colombia, Km 12 via Chapinero, Palmira, Colombia
- Department of Agriculture and Natural Sciences, Tennessee State University, Nashville, Tennessee, United States of America
| | | | - Claritza Muñóz
- Generation Challenge Program, Tropical Legumes I, c/o CIAT, Cali, Colombia
| | - Deissy K. Yuyó
- Departamento de Agronomía Universidad Nacional de Colombia, Facultad de Agronomía, Bogotá, Colombia
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Venturelli GL, Brod FCA, Rossi GB, Zimmermann NF, Oliveira JP, Faria JC, Arisi ACM. A Specific Endogenous Reference for Genetically Modified Common Bean (Phaseolus vulgaris L.) DNA Quantification by Real-Time PCR Targeting Lectin Gene. Mol Biotechnol 2014; 56:1060-8. [DOI: 10.1007/s12033-014-9786-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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López-Pedrouso M, Bernal J, Franco D, Zapata C. Evaluating two-dimensional electrophoresis profiles of the protein phaseolin as markers of genetic differentiation and seed protein quality in common bean (Phaseolus vulgaris L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:7200-7208. [PMID: 24983510 DOI: 10.1021/jf502439u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
High-resolution two-dimensional electrophoresis (2-DE) profiles of the protein phaseolin, the major seed storage protein of common bean, display great number of spots with differentially glycosylated and phosphorylated α- and β-type polypeptides. This work aims to test whether these complex profiles can be useful markers of genetic differentiation and seed protein quality in bean populations. The 2-DE phaseolin profile and the amino acid composition were examined in bean seeds from 18 domesticated and wild accessions belonging to the Mesoamerican and Andean gene pools. We found that proteomic distances based on 2-DE profiles were successful in identifying the accessions belonging to each gene pool and outliers distantly related. In addition, accessions identified as outliers from proteomic distances showed the highest levels of methionine content, an essential amino acid deficient in bean seeds. These findings suggest that 2-DE phaseolin profiles provide valuable information with potential of being used in common bean genetic improvement.
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Affiliation(s)
- María López-Pedrouso
- Department of Genetics, University of Santiago de Compostela , Santiago de Compostela-15782, Spain
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Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 2014; 46:707-13. [PMID: 24908249 PMCID: PMC7048698 DOI: 10.1038/ng.3008] [Citation(s) in RCA: 690] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 05/15/2014] [Indexed: 01/13/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.
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Affiliation(s)
- Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Sujan Mamidi
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - G Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Steven B Cannon
- US Department of Agriculture–Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Qijian Song
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | | | - Valerie Geffroy
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
- Institut National de la Recherche Agronomique (INRA), Université Paris–Sud, Unité Mixte de Recherche de Génétique Végétale, Gif-sur-Yvette, France
| | - Samira Mafi Moghaddam
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Matthew Blair
- Department of Agricultural and Natural Sciences, Tennessee State University, Nashville, Tennessee USA
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Mansi Chovatia
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, California USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Michael Gonzales
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - David L Hyten
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
- Present Address: Present addresses: Pioneer Hi-Bred International, Inc., Johnston, Iowa, USA (D.L.H.) and Genética e Melhoramento, Federal University of Viçosa, Viçosa, Brazil (J.R.).,
| | - Gaofeng Jia
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - James D Kelly
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan USA
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Manon M S Richard
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
| | - Phillip N Miklas
- US Department of Agriculture–Agricultural Research Service, Vegetable and Forage Crop Research Unit, Prosser, Washington USA
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Josiane Rodrigues
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
- Present Address: Present addresses: Pioneer Hi-Bred International, Inc., Johnston, Iowa, USA (D.L.H.) and Genética e Melhoramento, Federal University of Viçosa, Viçosa, Brazil (J.R.).,
| | - Vincent Thareau
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
| | - Carlos A Urrea
- Panhandle Research and Extension Center, University of Nebraska, Scottsbluff, Nebraska USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Yeisoo Yu
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Ming Zhang
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Rod A Wing
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Perry B Cregan
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - Daniel S Rokhsar
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
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Ceylan A, Öcal N, Akbulut M. Genetic diversity among the Turkish common bean cultivars (Phaseolus vulgaris L.) as assessed by SRAP, POGP and cpSSR markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Climer Vigueira C, Dobney K, Gremillion KJ, Barton L, Arroyo-Kalin M, Purugganan MD, Rubio de Casas R, Bollongino R, Burger J, Fuller DQ, Bradley DG, Balding DJ, Richerson PJ, Gilbert MTP, Larson G, Thomas MG. Storytelling and story testing in domestication. Proc Natl Acad Sci U S A 2014; 111:6159-64. [PMID: 24753572 PMCID: PMC4035932 DOI: 10.1073/pnas.1400425111] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The domestication of plants and animals marks one of the most significant transitions in human, and indeed global, history. Traditionally, study of the domestication process was the exclusive domain of archaeologists and agricultural scientists; today it is an increasingly multidisciplinary enterprise that has come to involve the skills of evolutionary biologists and geneticists. Although the application of new information sources and methodologies has dramatically transformed our ability to study and understand domestication, it has also generated increasingly large and complex datasets, the interpretation of which is not straightforward. In particular, challenges of equifinality, evolutionary variance, and emergence of unexpected or counter-intuitive patterns all face researchers attempting to infer past processes directly from patterns in data. We argue that explicit modeling approaches, drawing upon emerging methodologies in statistics and population genetics, provide a powerful means of addressing these limitations. Modeling also offers an approach to analyzing datasets that avoids conclusions steered by implicit biases, and makes possible the formal integration of different data types. Here we outline some of the modeling approaches most relevant to current problems in domestication research, and demonstrate the ways in which simulation modeling is beginning to reshape our understanding of the domestication process.
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Affiliation(s)
| | - Robin G. Allaby
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Nicole Boivin
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, Oxford OX1 3QY, United Kingdom
| | - Anna Rudzinski
- Research Department of Genetics, Evolution, and Environment and
| | - Ilaria M. Grimaldi
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, Oxford OX1 3QY, United Kingdom
| | - J. Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | | | - Keith Dobney
- Department of Archaeology, University of Aberdeen, Aberdeen AB24 3UF, United Kingdom
| | | | - Loukas Barton
- Department of Anthropology, Center for Comparative Archaeology, University of Pittsburgh, Pittsburgh, PA 15260
| | - Manuel Arroyo-Kalin
- Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom
| | - Michael D. Purugganan
- Department of Biology, New York University, New York, NY 10003-6688
- Center for Genomics and Systems Biology, New York University Abu Dhabi Research Institute, Abu Dhabi, United Arab Emirates
| | | | - Ruth Bollongino
- Institute of Anthropology, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Joachim Burger
- Institute of Anthropology, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Dorian Q. Fuller
- Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom
| | | | - David J. Balding
- University College London Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Peter J. Richerson
- Department of Environmental Science and Policy, University of California, Davis, CA 95616
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; and
| | - Greger Larson
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, United Kingdom
| | - Mark G. Thomas
- Research Department of Genetics, Evolution, and Environment and
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Yuste-Lisbona FJ, González AM, Capel C, García-Alcázar M, Capel J, De Ron AM, Lozano R, Santalla M. Genetic analysis of single-locus and epistatic QTLs for seed traits in an adapted × nuña RIL population of common bean (Phaseolus vulgaris L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:897-912. [PMID: 24441949 DOI: 10.1007/s00122-014-2265-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 01/03/2014] [Indexed: 05/13/2023]
Abstract
The QTLs analyses here reported demonstrate the significant role of both individual additive and epistatic effects in the genetic control of seed quality traits in the Andean common bean. Common bean shows considerable variability in seed size and coat color, which are important agronomic traits determining farmer and consumer acceptability. Therefore, strategies must be devised to improve the genetic base of cultivated germplasm with new alleles that would contribute positively to breeding programs. For that purpose, a population of 185 recombinant inbred lines derived from an Andean intra-gene pool cross, involving an adapted common bean (PMB0225 parent) and an exotic nuña bean (PHA1037 parent), was evaluated under six different--short and long-day--environmental conditions for seed dimension, weight, color, and brightness traits, as well as the number of seed per pod. A multi-environment Quantitative Trait Loci (QTL) analysis was carried out and 59 QTLs were mapped on all linkage groups, 18 of which had only individual additive effects, while 27 showed only epistatic effects and 14 had both individual additive and epistatic effects. Multivariate models that included significant QTL explained from 8 to 68 % and 2 to 15 % of the additive and epistatic effects, respectively. Most of these QTLs were consistent over environment, though interactions between QTLs and environments were also detected. Despite this, QTLs with differential effect on long-day and short-day environments were not found. QTLs identified were positioned in cluster, suggesting that either pleiotropic QTLs control several traits or tightly linked QTLs for different traits map together in the same genomic regions. Overall, our results show that digenic epistatic interactions clearly play an important role in the genetic control of seed quality traits in the Andean common bean.
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Affiliation(s)
- Fernando J Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL). Campus de Excelencia Internacional Agroalimentario, CeiA3, Universidad de Almería, 04120, Almería, Spain
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44
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Rao I. Advances in Improving Adaptation of Common Bean and Brachiaria Forage Grasses to Abiotic Stresses in the Tropics. BOOKS IN SOILS, PLANTS, AND THE ENVIRONMENT 2014. [DOI: 10.1201/b16675-49] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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45
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Diniz AL, Zucchi MI, Santini L, Benchimol-Reis LL, Fungaro MHP, Vieira MLC. Nucleotide diversity based on phaseolin and iron reductase genes in common bean accessions of different geographical origins. Genome 2014; 57:69-77. [PMID: 24702064 DOI: 10.1139/gen-2013-0183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Discriminating genotypes within plant collections is imperative, and DNA sequence approaches for detecting single nucleotide polymorphisms (SNPs) have proved essential in any modern analysis of germplasm. By sequencing the α-Phs and PvFRO1 genes that, respectively, encode phaseolin and an iron reductase, we prospected for SNPs in exonic and intronic regions of both genes in a sample of 31 accessions of Phaseolus vulgaris from Mesoamerican and Andean gene pools, and one accession of Phaseolus lunatus, chosen as an outgroup. Sequence alignment showed 95 SNPs in α-Phs and 83 in PvFRO1, but diversity along the nucleotide sequences was not evenly distributed in both genes. Accessions from the same gene pool showed greater similarity than those from different gene pools, and the cluster patterns obtained in this study were consistent with the hierarchical organization into two P. vulgaris gene pools. The polymorphisms detected in the α-Phs gene allowed better discrimination among the accessions within each cluster than the PvFRO1 polymorphisms. Furthermore, some variations within exons changes amino acids in both predicted protein sequences. In an unprecedented result, the phaseolin-predicted amino acid variation allowed most of the accessions to be typified.
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Affiliation(s)
- Augusto L Diniz
- a Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, P.O. Box 83, Piracicaba, 13418-900, Brazil
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Yuan JH, Cornille A, Giraud T, Cheng FY, Hu YH. Independent domestications of cultivated tree peonies from different wild peony species. Mol Ecol 2013; 23:82-95. [PMID: 24138195 DOI: 10.1111/mec.12567] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 11/30/2022]
Abstract
An understanding of plant domestication history provides insights into general mechanisms of plant adaptation and diversification and can guide breeding programmes that aim to improve cultivated species. Cultivated tree peonies (genus Paeonia L.) are among the most popular ornamental plants in the world; yet, the history of their domestication is still unresolved. Here, we explored whether the domestication in China of historically cultivated peonies, that is, the common and flare cultivated tree peonies, was a single event or whether independent domestications occurred. We used 14 nuclear microsatellite markers and a comprehensive set of 553 tree peonies collected across China, including common tree peonies, flare tree peonies and the wild species or subspecies that are potential contributors to the cultivated tree peonies, that is, Paeonia rockii ssp. rockii, P. rockii ssp. atava, P. jishanensis and P. decomposita. Assignment methods, a principal component analysis and approximate Bayesian computations provided clear evidence for independent domestications of these common tree and flare tree peonies from two distinct and allopatric wild species, P. jishanensis and P. rockii ssp. atava, respectively. This study provides the first example of independent domestications of cultivated trees from distinct species and locations. This work also yields crucial insight into the history of domestication of one of the most popular woody ornamental plants. The cultivated peonies represent an interesting case of parallel and convergent evolution. The information obtained in this study will be valuable both for improving current tree peony breeding strategies and for understanding the mechanisms of domestication, diversification and adaptation in plants.
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Affiliation(s)
- Jun-Hui Yuan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Shanghai, 201602, China; Landscape Architecture College, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China
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Roullier C, Duputié A, Wennekes P, Benoit L, Fernández Bringas VM, Rossel G, Tay D, McKey D, Lebot V. Disentangling the origins of cultivated sweet potato (Ipomoea batatas (L.) Lam.). PLoS One 2013; 8:e62707. [PMID: 23723970 PMCID: PMC3664560 DOI: 10.1371/journal.pone.0062707] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 03/27/2013] [Indexed: 11/18/2022] Open
Abstract
Sweet potato (Ipomoea batatas (L.) Lam., Convolvulaceae) counts among the most widely cultivated staple crops worldwide, yet the origins of its domestication remain unclear. This hexaploid species could have had either an autopolyploid origin, from the diploid I. trifida, or an allopolyploid origin, involving genomes of I. trifida and I. triloba. We generated molecular genetic data for a broad sample of cultivated sweet potatoes and its diploid and polyploid wild relatives, for noncoding chloroplast and nuclear ITS sequences, and nuclear SSRs. Our data did not support an allopolyploid origin for I. batatas, nor any contribution of I. triloba in the genome of domesticated sweet potato. I. trifida and I. batatas are closely related although they do not share haplotypes. Our data support an autopolyploid origin of sweet potato from the ancestor it shares with I. trifida, which might be similar to currently observed tetraploid wild Ipomoea accessions. Two I. batatas chloroplast lineages were identified. They show more divergence with each other than either does with I. trifida. We thus propose that cultivated I. batatas have multiple origins, and evolved from at least two distinct autopolyploidization events in polymorphic wild populations of a single progenitor species. Secondary contact between sweet potatoes domesticated in Central America and in South America, from differentiated wild I. batatas populations, would have led to the introgression of chloroplast haplotypes of each lineage into nuclear backgrounds of the other, and to a reduced divergence between nuclear gene pools as compared with chloroplast haplotypes.
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Affiliation(s)
- Caroline Roullier
- Unité Mixte de Recherche Amélioration et Adaptation des plantes (UMR AGAP), Centre International de Recherches en Agronomie pour le Développement (CIRAD), Montpellier, France
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Université Montpellier II, Montpellier, France
- * E-mail:
| | - Anne Duputié
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Paul Wennekes
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Laure Benoit
- Unité Mixte de Recherche Amélioration et Adaptation des plantes (UMR AGAP), Centre International de Recherches en Agronomie pour le Développement (CIRAD), Montpellier, France
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | | | | | - David Tay
- International Potato Center (CIP), Lima, Peru
| | - Doyle McKey
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Université Montpellier II, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Vincent Lebot
- Unité Mixte de Recherche Amélioration et Adaptation des plantes (UMR AGAP), Centre International de Recherches en Agronomie pour le Développement (CIRAD), Montpellier, France
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Use of Wild Relatives and Closely Related Species to Adapt Common Bean to Climate Change. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3020433] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Beebe SE, Rao IM, Blair MW, Acosta-Gallegos JA. Phenotyping common beans for adaptation to drought. Front Physiol 2013; 4:35. [PMID: 23507928 PMCID: PMC3589705 DOI: 10.3389/fphys.2013.00035] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 02/12/2013] [Indexed: 11/13/2022] Open
Abstract
Common beans (Phaseolus vulgaris L.) originated in the New World and are the grain legume of greatest production for direct human consumption. Common bean production is subject to frequent droughts in highland Mexico, in the Pacific coast of Central America, in northeast Brazil, and in eastern and southern Africa from Ethiopia to South Africa. This article reviews efforts to improve common bean for drought tolerance, referring to genetic diversity for drought response, the physiology of drought tolerance mechanisms, and breeding strategies. Different races of common bean respond differently to drought, with race Durango of highland Mexico being a major source of genes. Sister species of P. vulgaris likewise have unique traits, especially P. acutifolius which is well adapted to dryland conditions. Diverse sources of tolerance may have different mechanisms of plant response, implying the need for different methods of phenotyping to recognize the relevant traits. Practical considerations of field management are discussed including: trial planning; water management; and field preparation.
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Affiliation(s)
- Stephen E. Beebe
- CIAT—International Center for Tropical AgricultureCali, Colombia
| | | | - Matthew W. Blair
- Formerly of CIAT, CIAT—International Center for Tropical AgricultureCali, Colombia
| | - Jorge A. Acosta-Gallegos
- Bean Program, INIFAP Research Station, Instituto Nacional de Investigaciones Forestales, Agrícolas y PecuariasCelaya, Mexico
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Bitocchi E, Bellucci E, Giardini A, Rau D, Rodriguez M, Biagetti E, Santilocchi R, Spagnoletti Zeuli P, Gioia T, Logozzo G, Attene G, Nanni L, Papa R. Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. THE NEW PHYTOLOGIST 2013; 197:300-313. [PMID: 23126683 DOI: 10.1111/j.1469-8137.2012.04377.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/07/2012] [Indexed: 05/03/2023]
Abstract
We have studied the nucleotide diversity of common bean, Phaseolus vulgaris, which is characterized by two independent domestications in two geographically distinct areas: Mesoamerica and the Andes. This provides an important model, as domestication can be studied as a replicate experiment. We used nucleotide data from five gene fragments characterized by large introns to analyse 214 accessions (102 wild and 112 domesticated). The wild accessions represent a cross-section of the entire geographical distribution of P. vulgaris. A reduction in genetic diversity in both of these gene pools was found, which was three-fold greater in Mesoamerica compared with the Andes. This appears to be a result of a bottleneck that occurred before domestication in the Andes, which strongly impoverished this wild germplasm, leading to the minor effect of the subsequent domestication bottleneck (i.e. sequential bottleneck). These findings show the importance of considering the evolutionary history of crop species as a major factor that influences their current level and structure of genetic diversity. Furthermore, these data highlight a single domestication event within each gene pool. Although the findings should be interpreted with caution, this evidence indicates the Oaxaca valley in Mesoamerica, and southern Bolivia and northern Argentina in South America, as the origins of common bean domestication.
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Affiliation(s)
- Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Alessandro Giardini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Via de Nicola, 07100, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Via de Nicola, 07100, Sassari, Italy
| | - Eleonora Biagetti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Rodolfo Santilocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Pierluigi Spagnoletti Zeuli
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| | - Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| | - Giuseppina Logozzo
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Via de Nicola, 07100, Sassari, Italy
| | - Laura Nanni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Cereal Research Centre, Agricultural Research Council (CRA-CER), S.S. 16, Km 675, 71122, Foggia, Italy
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