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Ning W, Rogers KM, Hsu CY, Magbanua ZV, Pechanova O, Arick MA, Kayal E, Hu G, Peterson DG, Udall JA, Grover CE, Wendel JF. Origin and diversity of the wild cottons (Gossypium hirsutum) of Mound Key, Florida. Sci Rep 2024; 14:14046. [PMID: 38890398 PMCID: PMC11189519 DOI: 10.1038/s41598-024-64887-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Elucidating genetic diversity within wild forms of modern crops is essential for understanding domestication and the possibilities of wild germplasm utilization. Gossypium hirsutum is a predominant source of natural plant fibers and the most widely cultivated cotton species. Wild forms of G. hirsutum are challenging to distinguish from feral derivatives, and truly wild populations are uncommon. Here we characterize a population from Mound Key Archaeological State Park, Florida using genome-wide SNPs extracted from 25 individuals over three sites. Our results reveal that this population is genetically dissimilar from other known wild, landrace, and domesticated cottons, and likely represents a pocket of previously unrecognized wild genetic diversity. The unexpected level of divergence between the Mound Key population and other wild cotton populations suggests that the species may harbor other remnant and genetically distinct populations that are geographically scattered in suitable habitats throughout the Caribbean. Our work thus has broader conservation genetic implications and suggests that further exploration of natural diversity in this species is warranted.
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Affiliation(s)
- Weixuan Ning
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA, 50011, USA
| | - Karen M Rogers
- Division of Recreation and Parks, Florida Department of Environmental Protection, District 4 Administration, 1843 S. Tamiami Trail, Osprey, FL, 34229, USA
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Zenaida V Magbanua
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Olga Pechanova
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Ehsan Kayal
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA, 50011, USA
| | - Guanjing Hu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Joshua A Udall
- Crop Germplasm Research Unit, USDA/Agricultural Research Service, 2881 F&B Road, College Station, TX, 77845, USA
| | - Corrinne E Grover
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA, 50011, USA.
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Lee J, Kang YJ, Park H, Shim S, Ha J, Lee T, Kim MY, Lee SH. Unraveling the maternal and paternal origins of allotetraploid Vigna reflexo-pilosa. Sci Rep 2023; 13:22951. [PMID: 38135720 PMCID: PMC10746702 DOI: 10.1038/s41598-023-49908-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
The genomic structures of Vigna hirtella Ridl. and Vigna trinervia (B.Heyne ex Wight & Arn.) Tateishi & Maxted, key ancestral species of the allotetraploid Vigna reflexo-pilosa var. glabra (Roxb.) N.Tomooka & Maxted, remain poorly understood. This study presents a comprehensive genomic comparison of these species to deepen our knowledge of their evolutionary trajectories. By comparing the genomic profiles of V. hirtella and V. trinervia with those of V. reflexo-pilosa, we investigate the complex genomic mechanisms underlying allopolyploid evolution within the genus Vigna. Comparison of the chloroplast genome revealed that V. trinervia is closely related to V. reflexo-pilosa. De novo assembly of the whole genome, followed by synteny analysis and Ks value calculations, confirms that V. trinervia is closely related to the A genome of V. reflexo-pilosa, and V. hirtella to its B genome. Furthermore, the comparative analyses reveal that V. reflexo-pilosa retains residual signatures of a previous polyploidization event, particularly evident in higher gene family copy numbers. Our research provides genomic evidence for polyploidization within the genus Vigna and identifies potential donor species of allotetraploid species using de novo assembly techniques. Given the Southeast Asian distribution of both V. hirtella and V. trinervia, natural hybridization between these species, with V. trinervia as the maternal ancestor and V. hirtella as the paternal donor, seems plausible.
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Affiliation(s)
- Jayern Lee
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- , Macrogen, Seoul, Republic of Korea
| | - Yang Jae Kang
- Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, Jinju, Republic of Korea
- Division of Life Science Department at, Gyeongsang National University, Jinju, Republic of Korea
| | - Halim Park
- Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, Jinju, Republic of Korea
| | - Sangrea Shim
- Department of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Republic of Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | | | - Moon Young Kim
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Suk-Ha Lee
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.
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Wu YJ, Chen SY, Hsu FC, Wu WL, Hsieh TF, Su JF, Lai YH, Lai PC, Chen WH, Chen HH. PeCIN8 expression correlates with flower size and resistance to yellow leaf disease in Phalaenopsis orchids. BMC PLANT BIOLOGY 2023; 23:545. [PMID: 37936061 PMCID: PMC10629045 DOI: 10.1186/s12870-023-04567-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The orchid industry has seen a recent surge in export values due to the floral morphology and versatile applications of orchids in various markets for medicinal, food additive, and cosmetic usages. However, plant-related diseases, including the yellow leaf disease caused by Fusarium solani, have caused significant losses in the production value of Phalaenopsis (up to 30%). RESULTS In this study, 203 Phalaenopsis cultivars were collected from 10 local orchid nurseries, and their disease severity index and correlation with flower size were evaluated. Larger flowers had weaker resistance to yellow leaf disease, and smaller flowers had stronger resistance. For the genetic relationship of disease resistance to flower size, the genetic background of all cultivars was assessed using OrchidWiz Orchid Database Software and principal component analysis. In addition, we identified the orthologous genes of BraTCP4, namely PeIN6, PeCIN7, and PeCIN8, which are involved in resistance to pathogens, and analyzed their gene expression. The expression of PeCIN8 was significantly higher in the most resistant cultivars (A7403, A11294, and A2945) relative to the most susceptible cultivars (A10670, A6390, and A10746). CONCLUSIONS We identified a correlation between flower size and resistance to yellow leaf disease in Phalaenopsis orchids. The expression of PeCIN8 may regulate the two traits in the disease-resistant cultivars. These findings can be applied to Phalaenopsis breeding programs to develop resistant cultivars against yellow leaf disease.
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Affiliation(s)
- Yan-Jeng Wu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shu-Yun Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
- Present Address: Department of Agronomy, National Chung-Hsin University, Taichung, Taiwan
| | - Fu-Cheng Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wen-Luan Wu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ting-Fang Hsieh
- Plant Pathology Division, Taiwan Agricultural Research Institute, Ministry of Agriculture, Taichung, 413008, Taiwan
| | - Jiunn-Feng Su
- Plant Pathology Division, Taiwan Agricultural Research Institute, Ministry of Agriculture, Taichung, 413008, Taiwan
| | - Yung-Hsiang Lai
- Taida Horticultural Co., Ltd., Dacun Township, Changhua County, 515002, Taiwan
| | - Pen-Chih Lai
- Taida Horticultural Co., Ltd., Dacun Township, Changhua County, 515002, Taiwan
| | - Wen-Huei Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.
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Chacón-Fuentes M, Bardehle L, Seguel I, Espinoza J, Lizama M, Quiroz A. Herbivory Damage Increased VOCs in Wild Relatives of Murtilla Plants Compared to Their First Offspring. Metabolites 2023; 13:metabo13050616. [PMID: 37233657 DOI: 10.3390/metabo13050616] [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: 03/15/2023] [Revised: 04/10/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Murtilla (Ugni molinae) is a shrub native to Chile that has undergone an incipient domestication process aimed at increasing its productivity. The reduction in intrinsic chemical defenses due to the domestication process has resulted in a decrease in the plant's ability to defend itself against mechanical or insect damage. In response to this damage, plants release volatile organic compounds (VOCs) as a means of defense. To understand how domestication has impacted the production of VOCs in the first offspring of murtilla, we hypothesized that their levels would be reduced due to the induction of mechanical and herbivore damage. To test this hypothesis, we collected VOCs from four offspring ecotypes and three wild relatives of murtilla. We induced mechanical and herbivore damage in the plants and then enclosed them in a glass chamber, where we captured the VOCs. We identified 12 compounds using GC-MS. Our results showed that wild relative ecotypes had a higher VOC release rate of 624.6 µg/cm2/day. Herbivore damage was the treatment that produced the highest release of VOCs, with 439.3 µg/cm2/day in wild relatives. These findings suggest that herbivory triggers defenses through the emission of VOCs, and that domestication has influenced the production of these compounds in murtilla. Overall, this study contributes to bridging the gap in the incipient domestication history of murtilla and highlights the importance of considering the impact of domestication on a plant's chemical defenses.
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Affiliation(s)
| | - Leonardo Bardehle
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco 4811230, Chile
- Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco 4780000, Chile
- Departamento de Producción Agropecuaria, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco 4811230, Chile
| | - Ivette Seguel
- Innovalimentos SPA, Gabriela Mistral 02311, Temuco 4780000, Chile
| | - Javier Espinoza
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco 4811230, Chile
- Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco 4780000, Chile
| | - Marcelo Lizama
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile
| | - Andrés Quiroz
- Laboratorio de Química Ecológica, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco 4811230, Chile
- Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Av. Francisco Salazar 01145, Casilla 54-D, Temuco 4780000, Chile
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Xia Z, Dai X, Fan W, Liu C, Zhang M, Bian P, Zhou Y, Li L, Zhu B, Liu S, Li Z, Wang X, Yu M, Xiang Z, Jiang Y, Zhao A. Chromosome-level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1119-1137. [PMID: 36055564 DOI: 10.1016/j.gpb.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 07/02/2022] [Accepted: 08/23/2022] [Indexed: 12/13/2022]
Abstract
Multiple plant lineages have independently evolved sex chromosomes and variable karyotypes to maintain their sessile lifestyles through constant biological innovation. Morus notabilis, a dioecious mulberry species, has the fewest chromosomes among Morus spp., but the genetic basis of sex determination and karyotype evolution in this species has not been identified. In this study, three high-quality genome assemblies were generated for Morus spp. [including dioecious M. notabilis (male and female) and Morus yunnanensis (female)] with genome sizes of 301-329 Mb and were grouped into six pseudochromosomes. Using a combination of genomic approaches, we found that the putative ancestral karyotype of Morus species was close to 14 protochromosomes, and that several chromosome fusion events resulted in descending dysploidy (2n = 2x = 12). We also characterized a ∼ 6.2-Mb sex-determining region on chromosome 3. Four potential male-specific genes, a partially duplicatedDNA helicase gene (named MSDH) and three Ty3_Gypsy long terminal repeat retrotransposons (named MSTG1/2/3), were identified in the Y-linked area and considered to be strong candidate genes for sex determination or differentiation. Population genomic analysis showed that Guangdong accessions in China were genetically similar to Japanese accessions of mulberry. In addition, genomic areas containing selective sweeps that distinguish domesticated mulberry from wild populations in terms of flowering and disease resistance were identified. Our findings provide an important genetic resource for sex identification research and molecular breeding in mulberry.
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Affiliation(s)
- Zhongqiang Xia
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wei Fan
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China
| | - Meirong Zhang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Peipei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuping Zhou
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Liang Li
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Baozhong Zhu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Shuman Liu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Zhengang Li
- The Sericultural and Apicultural Research Institute, Yunnan Academy of Agricultural Sciences, Mengzi 661100, China
| | - Xiling Wang
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400716, China
| | - Maode Yu
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400716, China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Aichun Zhao
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China.
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Assessment of the Breeding Potential of a Set of Genotypes Selected from a Natural Population of Akebia trifoliata (Three–Leaf Akebia). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Akebia trifoliata (three-leaf akebia) has long been used as a medicinal herb and has the potential to be used in diverse ways, especially as a fruit crop. However, efforts to domesticate and cultivate new varieties for commercial use are only in their infancy. Here, we evaluated the genetic diversity of 29 genotypes, which were previously selected from a natural population consisting of 1447 genotypes and exhibiting high resistance to fungal diseases and a smooth peel of A. trifoliata using 85 genome-specific single sequence repeat (SSR) markers. We also characterized variation in 19 phenotypic traits and nutritional components. Large variation in phenotypic traits and nutritional components was observed, especially in vitamin C, seed/pulp, and fruit color. Correlation analyses revealed that many phenotypic traits and nutritional components were significantly correlated. A principal component analysis identified five principal components, which explained 83.2% of the total variation in the data. The results of the SSR analysis revealed that 80 of the 85 SSR markers were polymorphic; the total number of alleles amplified was 532. The expected heterozygosity was 0.672, and Shannon’s information index was 1.328. A Ward dendrogram and unweighted pair group method with arithmetic mean dendrogram revealed high diversity among the 29 genotypes and suggested that the measured morphological and nutritional traits were genetically independent of disease resistance and texture traits, as well as SSR marker loci. Finally, our results suggest that additional rounds of selection from the selected population, despite its small size, could be effective for the development of new A. trifoliata fruit cultivars.
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7
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Alves-Pereira A, Zucchi MI, Clement CR, Viana JPG, Pinheiro JB, Veasey EA, de Souza AP. Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties. Sci Rep 2022; 12:1268. [PMID: 35075210 PMCID: PMC8786832 DOI: 10.1038/s41598-022-05160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/05/2022] [Indexed: 11/09/2022] Open
Abstract
Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world's major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc's wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop's domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc's evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.
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Affiliation(s)
- Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia Dos Agronegócios (APTA), Pólo Centro-Sul. Rodovia SP 127, km 30, Piracicaba, SP, 13400-970, Brazil
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM, 69067-375, Brazil
| | - João Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois at Urbana-Champaign (UIUC), AW-101 Turner Hall, 1102 South Goodwin Avenue, Urbana, IL, 61801-4798, USA
| | - José Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil. .,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.
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Progressive Genomic Approaches to Explore Drought- and Salt-Induced Oxidative Stress Responses in Plants under Changing Climate. PLANTS 2021; 10:plants10091910. [PMID: 34579441 PMCID: PMC8471759 DOI: 10.3390/plants10091910] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 11/17/2022]
Abstract
Drought and salinity are the major environmental abiotic stresses that negatively impact crop development and yield. To improve yields under abiotic stress conditions, drought- and salinity-tolerant crops are key to support world crop production and mitigate the demand of the growing world population. Nevertheless, plant responses to abiotic stresses are highly complex and controlled by networks of genetic and ecological factors that are the main targets of crop breeding programs. Several genomics strategies are employed to improve crop productivity under abiotic stress conditions, but traditional techniques are not sufficient to prevent stress-related losses in productivity. Within the last decade, modern genomics studies have advanced our capabilities of improving crop genetics, especially those traits relevant to abiotic stress management. This review provided updated and comprehensive knowledge concerning all possible combinations of advanced genomics tools and the gene regulatory network of reactive oxygen species homeostasis for the appropriate planning of future breeding programs, which will assist sustainable crop production under salinity and drought conditions.
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9
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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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Advances in Genomics Approaches Shed Light on Crop Domestication. PLANTS 2021; 10:plants10081571. [PMID: 34451616 PMCID: PMC8401213 DOI: 10.3390/plants10081571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 11/18/2022]
Abstract
Crop domestication occurred ~10,000–12,000 years ago when humans shifted from a hunter–gatherer to an agrarian society. Crops were domesticated by selecting the traits in wild plant species that were suitable for human use. Research is crucial to elucidate the mechanisms and processes involved in modern crop improvement and breeding. Recent advances in genomics have revolutionized our understanding of crop domestication. In this review, we summarized cutting-edge crop domestication research by presenting its (1) methodologies, (2) current status, (3) applications, and (4) perspectives. Advanced genomics approaches have clarified crop domestication processes and mechanisms, and supported crop improvement.
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Fernie AR, Alseekh S, Liu J, Yan J. Using precision phenotyping to inform de novo domestication. PLANT PHYSIOLOGY 2021; 186:1397-1411. [PMID: 33848336 PMCID: PMC8260140 DOI: 10.1093/plphys/kiab160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/22/2021] [Indexed: 05/09/2023]
Abstract
An update on the use of precision phenotyping to assess the potential of lesser cultivated species as candidates for de novo domestication or similar development for future agriculture.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Author for communication: (A.R.F.)
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
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12
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Ren G, Zhang X, Li Y, Ridout K, Serrano-Serrano ML, Yang Y, Liu A, Ravikanth G, Nawaz MA, Mumtaz AS, Salamin N, Fumagalli L. Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa. SCIENCE ADVANCES 2021; 7:7/29/eabg2286. [PMID: 34272249 PMCID: PMC8284894 DOI: 10.1126/sciadv.abg2286] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/03/2021] [Indexed: 05/07/2023]
Abstract
Cannabis sativa has long been an important source of fiber extracted from hemp and both medicinal and recreational drugs based on cannabinoid compounds. Here, we investigated its poorly known domestication history using whole-genome resequencing of 110 accessions from worldwide origins. We show that C. sativa was first domesticated in early Neolithic times in East Asia and that all current hemp and drug cultivars diverged from an ancestral gene pool currently represented by feral plants and landraces in China. We identified candidate genes associated with traits differentiating hemp and drug cultivars, including branching pattern and cellulose/lignin biosynthesis. We also found evidence for loss of function of genes involved in the synthesis of the two major biochemically competing cannabinoids during selection for increased fiber production or psychoactive properties. Our results provide a unique global view of the domestication of C. sativa and offer valuable genomic resources for ongoing functional and molecular breeding research.
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Affiliation(s)
- Guangpeng Ren
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland.
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Kate Ridout
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Martha L Serrano-Serrano
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Ai Liu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Gudasalamani Ravikanth
- Suri Sehgal Center for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment, Royal Enclave Srirampura, Jakkur Post, Bangalore 560 064, India
| | - Muhammad Ali Nawaz
- Department of Biological and Environmental Sciences, Qatar University, Doha, Qatar
- Department of Zoology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Abdul Samad Mumtaz
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, 1015 Lausanne, Switzerland
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland.
- Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
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13
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Martínez-González C, Castellanos-Morales G, Barrera-Redondo J, Sánchez-de la Vega G, Hernández-Rosales HS, Gasca-Pineda J, Aguirre-Planter E, Moreno-Letelier A, Escalante AE, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Recent and Historical Gene Flow in Cultivars, Landraces, and a Wild Taxon of Cucurbita pepo in Mexico. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.656051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the test of introgression between lineages, we found that all possible arrangements for ancestral and derived sites between the lineages showed similar frequencies; thus, incomplete lineage sorting, but also gene flow, might be taking place in C. pepo. Overall, our results suggest that gene flow between these subspecies and cultigens, incomplete lineage sorting and the retention of ancestral characters shaped the evolutionary trajectory of C. pepo in its area of origin and diversification. In addition, we found evidence of the use of Mexican landraces as genetic material for the improvement of commercial cultivars. The landraces of Mexico are an important source of genetic diversity for C. pepo, which has been preserved both by management practices of small farmers and by the natural gene flow that exists between the different crop fields of the region.
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14
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Back to the Origins: Background and Perspectives of Grapevine Domestication. Int J Mol Sci 2021; 22:ijms22094518. [PMID: 33926017 PMCID: PMC8123694 DOI: 10.3390/ijms22094518] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
Domestication is a process of selection driven by humans, transforming wild progenitors into domesticated crops. The grapevine (Vitis vinifera L.), besides being one of the most extensively cultivated fruit trees in the world, is also a fascinating subject for evolutionary studies. The domestication process started in the Near East and the varieties obtained were successively spread and cultivated in different areas. Whether the domestication occurred only once, or whether successive domestication events occurred independently, is a highly debated mystery. Moreover, introgression events, breeding and intense trade in the Mediterranean basin have followed, in the last thousands of years, obfuscating the genetic relationships. Although a succession of studies has been carried out to explore grapevine origin and different evolution models are proposed, an overview of the topic remains pending. We review here the findings obtained in the main phylogenetic and genomic studies proposed in the last two decades, to clarify the fundamental questions regarding where, when and how many times grapevine domestication took place. Finally, we argue that the realization of the pan-genome of grapes could be a useful resource to discover and track the changes which have occurred in the genomes and to improve our understanding about the domestication.
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15
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Domestication of Plants of Ugni molinae Turcz (Myrtaceae) Interferes in the Biology of Chilesia rudis (Lepidoptera: Erebidae) Larvae. Molecules 2021; 26:molecules26072063. [PMID: 33916795 PMCID: PMC8038363 DOI: 10.3390/molecules26072063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 11/17/2022] Open
Abstract
In terms of the domestication process in murtilla, studies have found changes in the concentration of phenolic compounds, with reduction of chemical defense of plants, depending on the change in the feeding behavior of insects. Thus, we hypothesized that the domestication of Ugni molinae decreases the content of phenolic compounds and modifies the feeding preference of Chilesia rudis larvae. Leaves of three parental ecotypes and four cultivated ecotypes were used in preference experiments to evaluate the mass gain and leaves consumption of larvae. Phenolic extracts from leaves of U. molinae were analyzed by HPLC. Identified compounds were incorporated in an artificial diet to assess their effect on mass gain, consumption, and survival of the larvae. The presence of phenolic compounds in bodies and feces was also evaluated. In terms of choice assays, larvae preferred parental ecotypes. Regarding compounds, vanillin was the most varied between the ecotypes in leaves. However, plant domestication did not show a reduction in phenolic compound concentration of the ecotypes studied. Furthermore, there was no clear relation between phenolic compounds and the performance of C. rudis larvae. Whether this was because of sequestration of some compounds by larvae is unknown. Finally, results of this study could also suggest that studied phenolic compounds have no role in the C. rudis larvae resistance in this stage of murtilla domestication process.
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16
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Fuller DQ, Barron A, Champion L, Dupuy C, Commelin D, Raimbault M, Denham T. Transition From Wild to Domesticated Pearl Millet ( Pennisetum glaucum) Revealed in Ceramic Temper at Three Middle Holocene Sites in Northern Mali. THE AFRICAN ARCHAEOLOGICAL REVIEW 2021; 38:211-230. [PMID: 34720323 PMCID: PMC8550313 DOI: 10.1007/s10437-021-09428-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 06/08/2023]
Abstract
Imprints of domesticated pearl millet (Pennisetum glaucum (L.) R. Br.) spikelets, observed as temper in ceramics dating to the third millennium BC, provide the earliest evidence for the cultivation and domestication process of this crop in northern Mali. Additional sherds from the same region dating to the fifth and fourth millennium BC were examined and found to have pearl millet chaff with wild morphologies. In addition to studying sherds by stereomicroscopy and subjecting surface casts to scanning electron microscopy (SEM), we also deployed X-ray microcomputed tomography (microCT) on eleven sherds. This significantly augmented the total dataset of archaeological pearl millet chaff remains from which to document the use of the wild pearl millet as ceramic temper and the evolution of its morphology over time. Grain sizes were also estimated from spikelets preserved in the ceramics. Altogether, we are now able to chart the evolution of domesticated pearl millet in western Africa using three characteristics: the evolution of nonshattering stalked involucres; the appearance of multiple spikelet involucres, usually paired spikelets; and the increase in grain size. By the fourth millennium BC, average grain breadth had increased by 28%, although spikelet features otherwise resemble the wild type. In the third millennium BC, the average width of seeds is 38% greater than that of wild seeds, while other qualitative features of domestication are indicated by the presence of paired spikelets and the appearance of nondehiscent, stalked involucres. Nonshattering spikelets had probably become fixed by around 2000 BC, while increases in average grain size continued into the second millennium BC. These data now provide a robust sequence for the morphological evolution of domesticated pearl millet, the first indigenous crop domesticated in western Africa. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10437-021-09428-8.
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Affiliation(s)
- Dorian Q. Fuller
- Institute of Archaeology, University College London, 31–34 Gordon Square, London, WC1H 0PY UK
- School of Cultural Heritage, Northwest University, Xi’an, China
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aleese Barron
- School of Archaeology and Anthropology, Australian National University, Banks Building, Canberra, ACT 2601 Australia
| | - Louis Champion
- Institute of Archaeological Sciences, Goethe University, Norbert-Wollheim-Platz 1, 60629 Frankfurt am Main, Germany
- Laboratoire Archéologie et Peuplement de l’Afrique (APA), Anthropology Unit of the Department of Genetics and Evolution (GenEv), University of Geneva, Geneva, Switzerland
| | - Christian Dupuy
- Institut des Mondes Africains (IMAF, UMR 8171, CNRS), Paris, France
| | - Dominique Commelin
- Laboratoire Méditerranéen de Préhistoire Europe Afrique (LAMPEA, UMR 7269 CNRS, Aix-en-Provence, France
| | - Michel Raimbault
- Laboratoire Méditerranéen de Préhistoire Europe Afrique (LAMPEA, UMR 7269 CNRS, Aix-en-Provence, France
| | - Tim Denham
- School of Archaeology and Anthropology, Australian National University, Banks Building, Canberra, ACT 2601 Australia
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17
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Garcia T, Duitama J, Zullo SS, Gil J, Ariani A, Dohle S, Palkovic A, Skeen P, Bermudez-Santana CI, Debouck DG, Martínez-Castillo J, Gepts P, Chacón-Sánchez MI. Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nat Commun 2021; 12:702. [PMID: 33514713 PMCID: PMC7846787 DOI: 10.1038/s41467-021-20921-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.
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Affiliation(s)
- Tatiana Garcia
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,grid.17088.360000 0001 2150 1785Present Address: Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI USA
| | - Jorge Duitama
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Stephanie Smolenski Zullo
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Juanita Gil
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia ,grid.411017.20000 0001 2151 0999Present Address: Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR USA
| | - Andrea Ariani
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA ,Present Address: BASF BBCC - Innovation Center, Gent, Belgium
| | - Sarah Dohle
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Antonia Palkovic
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Paola Skeen
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,Present Address: Nunhems USA, Vegetable Seeds BASF, Acampo, CA USA
| | - Clara Isabel Bermudez-Santana
- grid.10689.360000 0001 0286 3748Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel G. Debouck
- grid.418348.20000 0001 0943 556XCentro Internacional de Agricultura Tropical, Cali, Colombia
| | - Jaime Martínez-Castillo
- grid.418270.80000 0004 0428 7635Centro de Investigación Científica de Yucatán, Yucatán, Mexico
| | - Paul Gepts
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Maria Isabel Chacón-Sánchez
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
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18
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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19
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The seed water content as a time-independent physiological trait during germination in wild tree species such as Ceiba aesculifolia. Sci Rep 2020; 10:10429. [PMID: 32591557 PMCID: PMC7319967 DOI: 10.1038/s41598-020-66759-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022] Open
Abstract
Seeds constitute a key physiological stage in plants life cycle. During seed germination, there is a spatial-temporal imbibition pattern that correlates with described physiological processes. However, only the moment of testa rupture has been described as a critical, discrete stage. Could a specific relative water content (RWC) value reflect a physiological stage useful for comparisons between seed batches? We tracked seed-by-seed imbibition during germination to homogenize sampling and selected a transcriptomic approach to analyse the physiological transitions that occur in seed batches collected in different years and with contrasting phenotypic responses to a priming treatment. The seed RWC reflected the transcriptional transitions that occur during germination, regardless of imbibition time or collection year, and revealed a set of biological processes that occur in the dry seed and during early germination are associated with the phenotypic response to priming. As climate shifts, so do the timing of developmental events important for determining organismal fitness, and poses another challenge to the comprehension of molecular and physiological processes driving the interaction between organisms and environment. In this study, we demonstrate that the use of physiological traits, specific to a particular developmental stage, is a reliable time-independent approach.
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20
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Fatiukha A, Klymiuk V, Peleg Z, Saranga Y, Cakmak I, Krugman T, Korol AB, Fahima T. Variation in phosphorus and sulfur content shapes the genetic architecture and phenotypic associations within the wheat grain ionome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 98:667-679. [PMID: 31571297 DOI: 10.1111/tpj.14264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 05/27/2023]
Abstract
Dissection of the genetic basis of wheat ionome is crucial for understanding the physiological and biochemical processes underlying mineral accumulation in seeds, as well as for efficient crop breeding. Most of the elements essential for plants are metals stored in seeds as chelate complexes with phytic acid or sulfur-containing compounds. We assume that the involvement of phosphorus and sulfur in metal chelation is the reason for strong phenotypic correlations within ionome. Adjustment of element concentrations for the effect of variation in phosphorus and sulfur seed content resulted in drastic change of phenotypic correlations between the elements. The genetic architecture of wheat grain ionome was characterized by quantitative trait loci (QTL) analysis using a cross between durum and wild emmer wheat. QTL analysis of the adjusted traits and two-trait analysis of the initial traits paired with either P or S considerably improved QTL detection power and accuracy, resulting in the identification of 105 QTLs and 617 QTL effects for 11 elements. Candidate gene search revealed some potential functional associations between QTLs and corresponding genes within their intervals. Thus, we have shown that accounting for variation in P and S is crucial for understanding of the physiological and genetic regulation of mineral composition of wheat grain ionome and can be implemented for other plants.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
| | - Zvi Peleg
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Yehoshua Saranga
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Ismail Cakmak
- Faculty of Engineering & Natural Sciences, Sabanci University, Tuzla İstanbul, 34956, Turkey
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
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21
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Alves‐Pereira A, Clement CR, Picanço‐Rodrigues D, Veasey EA, Dequigiovanni G, Ramos SLF, Pinheiro JB, de Souza AP, Zucchi MI. A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia. Evol Appl 2020; 13:342-361. [PMID: 31993081 PMCID: PMC6976959 DOI: 10.1111/eva.12873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/14/2019] [Indexed: 12/19/2022] Open
Abstract
Amazonia is a major world centre of plant domestication, but the genetics of domestication remains unclear for most Amazonian crops. Manioc (Manihot esculenta) is the most important staple food crop that originated in this region. Although manioc is relatively well-studied, little is known about the diversification of bitter and sweet landraces and how they were dispersed across Amazonia. We evaluated single nucleotide polymorphisms (SNPs) in wild and cultivated manioc to identify outlier SNPs putatively under selection and to assess the neutral genetic structure of landraces to make inferences about the evolution of the crop in Amazonia. Some outlier SNPs were in putative manioc genes possibly related to plant architecture, transcriptional regulation and responses to stress. The neutral SNPs revealed contrasting genetic structuring for bitter and sweet landraces. The outlier SNPs may be signatures of the genomic changes resulting from domestication, while the neutral genetic structure suggests independent dispersals for sweet and bitter manioc, possibly related to the earlier domestication and diversification of the former. Our results highlight the role of ancient peoples and current smallholders in the management and conservation of manioc genetic diversity, including putative genes and specific genetic resources with adaptive potential in the context of climate change.
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Affiliation(s)
- Alessandro Alves‐Pereira
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
| | | | | | - Elizabeth Ann Veasey
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Gabriel Dequigiovanni
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Santiago Linorio Ferreyra Ramos
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - José Baldin Pinheiro
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Anete Pereira de Souza
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
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22
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Parker TA, Berny Mier Y Teran JC, Palkovic A, Jernstedt J, Gepts P. Pod indehiscence is a domestication and aridity resilience trait in common bean. THE NEW PHYTOLOGIST 2020; 225:558-570. [PMID: 31486530 DOI: 10.1111/nph.16164] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/14/2019] [Indexed: 05/05/2023]
Abstract
Plant domestication has strongly modified crop morphology and development. Nevertheless, many crops continue to display atavistic characteristics that were advantageous to their wild ancestors but are deleterious under cultivation, such as pod dehiscence (PD). Here, we provide the first comprehensive assessment of the inheritance of PD in the common bean (Phaseolus vulgaris), a major domesticated grain legume. Using three methods to evaluate the PD phenotype, we identified multiple, unlinked genetic regions controlling PD in a biparental population and two diversity panels. Subsequently, we assessed patterns of orthology among these loci and those controlling the trait in other species. Our results show that different genes were selected in each domestication and ecogeographic race. A chromosome Pv03 dirigent-like gene, involved in lignin biosynthesis, showed a base-pair substitution that is associated with decreased PD. This haplotype may underlie the expansion of Mesoamerican domesticates into northern Mexico, where arid conditions promote PD. The rise in frequency of the decreased-PD haplotype may be a consequence of the markedly different fitness landscape imposed by domestication. Environmental dependency and genetic redundancy can explain the maintenance of atavistic traits under domestication.
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Affiliation(s)
- Travis A Parker
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Jorge C Berny Mier Y Teran
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Antonia Palkovic
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Judy Jernstedt
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
| | - Paul Gepts
- Department of Plant Sciences / MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA
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23
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Melotto M, Brandl MT, Jacob C, Jay-Russell MT, Micallef SA, Warburton ML, Van Deynze A. Breeding Crops for Enhanced Food Safety. FRONTIERS IN PLANT SCIENCE 2020; 11:428. [PMID: 32351531 PMCID: PMC7176021 DOI: 10.3389/fpls.2020.00428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/24/2020] [Indexed: 05/12/2023]
Abstract
An increasing global population demands a continuous supply of nutritious and safe food. Edible products can be contaminated with biological (e.g., bacteria, virus, protozoa), chemical (e.g., heavy metals, mycotoxins), and physical hazards during production, storage, transport, processing, and/or meal preparation. The substantial impact of foodborne disease outbreaks on public health and the economy has led to multidisciplinary research aimed to understand the biology underlying the different contamination processes and how to mitigate food hazards. Here we review the knowledge, opportunities, and challenges of plant breeding as a tool to enhance the food safety of plant-based food products. First, we discuss the significant effect of plant genotypic and phenotypic variation in the contamination of plants by heavy metals, mycotoxin-producing fungi, and human pathogenic bacteria. In addition, we discuss the various factors (i.e., temperature, relative humidity, soil, microbiota, cultural practices, and plant developmental stage) that can influence the interaction between plant genetic diversity and contaminant. This exposes the necessity of a multidisciplinary approach to understand plant genotype × environment × microbe × management interactions. Moreover, we show that the numerous possibilities of crop/hazard combinations make the definition and identification of high-risk pairs, such as Salmonella-tomato and Escherichia coli-lettuce, imperative for breeding programs geared toward improving microbial safety of produce. Finally, we discuss research on developing effective assays and approaches for selecting desirable breeding germplasm. Overall, it is recognized that although breeding programs for some human pathogen/toxin systems are ongoing (e.g., Fusarium in wheat), it would be premature to start breeding when targets and testing systems are not well defined. Nevertheless, current research is paving the way toward this goal and this review highlights advances in the field and critical points for the success of this initiative that were discussed during the Breeding Crops for Enhanced Food Safety workshop held 5-6 June 2019 at University of California, Davis.
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Affiliation(s)
- Maeli Melotto
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- *Correspondence: Maeli Melotto,
| | - Maria T. Brandl
- United States Department of Agriculture-Agricultural Research Service, Produce Safety and Microbiology Research, Albany, CA, United States
| | - Cristián Jacob
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Michele T. Jay-Russell
- Western Center for Food Safety, University of California, Davis, Davis, CA, United States
| | - Shirley A. Micallef
- Department of Plant Science and Landscape Architecture, Center for Food Safety and Security Systems, University of Maryland, College Park, MD, United States
| | - Marilyn L. Warburton
- United States Department of Agriculture-Agricultural Research Service, Corn Host Plant Research Resistance Unit Mississippi State, Starkville, MS, United States
| | - Allen Van Deynze
- Plant Breeding Center, Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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24
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Gros‐Balthazard M, Besnard G, Sarah G, Holtz Y, Leclercq J, Santoni S, Wegmann D, Glémin S, Khadari B. Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:143-157. [PMID: 31192486 PMCID: PMC6851578 DOI: 10.1111/tpj.14435] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/11/2023]
Abstract
The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio-economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA-sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two-step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits.
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Affiliation(s)
- Muriel Gros‐Balthazard
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Present address:
New York University Abu Dhabi (NYUAD), Center for Genomics and Systems BiologySaadiyat IslandAbu DhabiUnited Arab Emirates
| | | | - Gautier Sarah
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Yan Holtz
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Julie Leclercq
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Sylvain Santoni
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Sylvain Glémin
- CNRSUniversité de RennesECOBIO (Ecosystèmes, biodiversité, évolution) − UMR 6553F‐35000RennesFrance
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Bouchaib Khadari
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Conservatoire Botanique National MéditerranéenUMR AGAPMontpellierFrance
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25
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Castellanos-Morales G, Ruiz-Mondragón KY, Hernández-Rosales HS, Sánchez-de la Vega G, Gámez N, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Tracing back the origin of pumpkins (Cucurbita pepo ssp. pepo L.) in Mexico. Proc Biol Sci 2019; 286:20191440. [PMID: 31409251 PMCID: PMC6710597 DOI: 10.1098/rspb.2019.1440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/23/2019] [Indexed: 11/12/2022] Open
Abstract
Cucurbita pepo is an economically important crop, which consists of cultivated C. pepo ssp. pepo, and two wild taxa (C. pepo ssp. fraterna and C. pepo ssp. ovifera). We aimed at understanding the domestication and the diversity of C. pepo in Mexico. We used two chloroplast regions and nine nuclear microsatellite loci to assess the levels of genetic variation and structure for C. pepo ssp. pepo's landraces sampled in 13 locations in Mexico, five improved varieties, one C. pepo ssp. fraterna population and ornamental C. pepo ssp. ovifera. We tested four hypotheses regarding the origin of C. pepo ssp. pepo's ancestor through approximate Bayesian computation: C. pepo ssp. ovifera as the ancestor; C. pepo ssp. fraterna as the ancestor; an unknown extinct lineage as the ancestor; and C. pepo ssp. pepo as hybrid from C. pepo ssp. ovifera and C. pepo ssp. fraterna ancestors. Cucurbita pepo ssp. pepo showed high genetic variation and low genetic differentiation. Cucurbita pepo ssp. fraterna and C. pepo ssp. pepo shared two chloroplast haplotypes. The three subspecies were well differentiated for microsatellite loci. Cucurbita pepo ssp. fraterna was probably C. pepo ssp. pepo's wild ancestor, but subsequent hybridization between taxa complicate defining C. pepo ssp. pepo's ancestor.
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Affiliation(s)
- Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Unidad Villahermosa, Villahermosa, Tabasco, Mexico
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
- UBIPRO, Facultad de Estudios Superiores, Iztacala, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Karen Y. Ruiz-Mondragón
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Helena S. Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Niza Gámez
- Facultad de Estudios Superiores, Zaragoza, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarías (INIFAP), Celaya, Guanajuato, Mexico
| | - Rafael Lira-Saade
- UBIPRO, Facultad de Estudios Superiores, Iztacala, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Coyoacán, Mexico
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26
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Fernie AR, Yan J. De Novo Domestication: An Alternative Route toward New Crops for the Future. MOLECULAR PLANT 2019; 12:615-631. [PMID: 30999078 DOI: 10.1016/j.molp.2019.03.016] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 05/19/2023]
Abstract
Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration. Moreover, the increase in human population size and dietary changes are putting an ever greater burden on agriculture. The majority of this burden is met by the cultivation of a very small number of species, largely in locations that differ from their origin of domestication. Recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable low-input agriculture. Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.
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Affiliation(s)
- Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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27
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Hufford MB, Berny Mier Y Teran JC, Gepts P. Crop Biodiversity: An Unfinished Magnum Opus of Nature. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:727-751. [PMID: 31035827 DOI: 10.1146/annurev-arplant-042817-040240] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Crop biodiversity is one of the major inventions of humanity through the process of domestication. It is also an essential resource for crop improvement to adapt agriculture to ever-changing conditions like global climate change and consumer preferences. Domestication and the subsequent evolution under cultivation have profoundly shaped the genetic architecture of this biodiversity. In this review, we highlight recent advances in our understanding of crop biodiversity. Topics include the reduction of genetic diversity during domestication and counteracting factors, a discussion of the relationship between parallel phenotypic and genotypic evolution, the role of plasticity in genotype × environment interactions, and the important role subsistence farmers play in actively maintaining crop biodiversity and in participatory breeding. Linking genotype and phenotype remains the holy grail of crop biodiversity studies.
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Affiliation(s)
- Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011-1020, USA;
| | | | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, California 95616-8780, USA; ,
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28
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Weller JL, Vander Schoor JK, Perez-Wright EC, Hecht V, González AM, Capel C, Yuste-Lisbona FJ, Lozano R, Santalla M. Parallel origins of photoperiod adaptation following dual domestications of common bean. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1209-1219. [PMID: 31222352 DOI: 10.1093/jxb/ery455] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/09/2019] [Indexed: 05/02/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important grain legume domesticated independently in Mexico and Andean South America approximately 8000 years ago. Wild forms are obligate short-day plants, and relaxation of photoperiod sensitivity was important for expansion to higher latitudes and subsequent global spread. To better understand the nature and origin of this key adaptation, we examined its genetic control in progeny of a wide cross between a wild accession and a photoperiod-insensitive cultivar. We found that photoperiod sensitivity is under oligogenic control, and confirm a major effect of the Ppd locus on chromosome 1. The red/far-red photoreceptor gene PHYTOCHROME A3 (PHYA3) was identified as a strong positional candidate for Ppd, and sequencing revealed distinct deleterious PHYA3 mutations in photoperiod-insensitive Andean and Mesoamerican accessions. These results reveal the independent origins of photoperiod insensitivity within the two major common bean gene pools and demonstrate the conserved importance of PHYA genes in photoperiod adaptation of short-day legume species.
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Affiliation(s)
- James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | | | | | - Valérie Hecht
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Ana M González
- Grupo de Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, Pontevedra, Spain
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almeria, Almeria, Spain
| | - Fernando J Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almeria, Almeria, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almeria, Almeria, Spain
| | - Marta Santalla
- Grupo de Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, Pontevedra, Spain
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29
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30
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Mousavi-Derazmahalleh M, Nevado B, Bayer PE, Filatov DA, Hane JK, Edwards D, Erskine W, Nelson MN. The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2543-2554. [PMID: 30225643 PMCID: PMC6244526 DOI: 10.1007/s00122-018-3171-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/25/2018] [Indexed: 05/21/2023]
Abstract
This study revealed that the western Mediterranean provided the founder population for domesticated narrow-leafed lupin and that genetic diversity decreased significantly during narrow-leafed lupin domestication. The evolutionary history of plants during domestication profoundly shaped the genome structure and genetic diversity of today's crops. Advances in next-generation sequencing technologies allow unprecedented opportunities to understand genome evolution in minor crops, which constitute the majority of plant domestications. A diverse set of 231 wild and domesticated narrow-leafed lupin (Lupinus angustifolius L.) accessions were subjected to genotyping-by-sequencing using diversity arrays technology. Phylogenetic, genome-wide divergence and linkage disequilibrium analyses were applied to identify the founder population of domesticated narrow-leafed lupin and the genome-wide effect of domestication on its genome. We found wild western Mediterranean population as the founder of domesticated narrow-leafed lupin. Domestication was associated with an almost threefold reduction in genome diversity in domesticated accessions compared to their wild relatives. Selective sweep analysis identified no significant footprints of selection around domestication loci. A genome-wide association study identified single nucleotide polymorphism markers associated with pod dehiscence. This new understanding of the genomic consequences of narrow-leafed lupin domestication along with molecular marker tools developed here will assist plant breeders more effectively access wild genetic diversity for crop improvement.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Philipp E Bayer
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - James K Hane
- CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin University, Bentley, WA, 6102, Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - William Erskine
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Matthew N Nelson
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK.
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31
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Su T, Wang W, Li P, Zhang B, Li P, Xin X, Sun H, Yu Y, Zhang D, Zhao X, Wen C, Zhou G, Wang Y, Zheng H, Yu S, Zhang F. A Genomic Variation Map Provides Insights into the Genetic Basis of Spring Chinese Cabbage (Brassica rapa ssp. pekinensis) Selection. MOLECULAR PLANT 2018; 11:1360-1376. [PMID: 30217779 DOI: 10.1016/j.molp.2018.08.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 05/08/2023]
Abstract
Chinese cabbage is the most consumed leafy crop in East Asian countries. However, premature bolting induced by continuous low temperatures severely decreases the yield and quality of the Chinese cabbage, and therefore restricts its planting season and geographic distribution. In the past 40 years, spring Chinese cabbage with strong winterness has been selected to meet the market demand. Here, we report a genome variation map of Chinese cabbage generated from the resequencing data of 194 geographically diverse accessions of three ecotypes. In-depth analyses of the selection sweeps and genome-wide patterns revealed that spring Chinese cabbage was selected from a specific population of autumn Chinese cabbage around the area of Shandong peninsula in northern China. We identified 23 genomic loci that underwent intensive selection, and further demonstrated by gene expression and haplotype analyses that the incorporation of elite alleles of VERNALISATION INSENTIVE 3.1 (BrVIN3.1) and FLOWER LOCUS C 1 (BrFLC1) is a determinant genetic source of variation during selection. Moreover, we showed that the quantitative response of BrVIN3.1 to cold due to the sequence variations in the cis elements of the BrVIN3.1 promoter significantly contributes to bolting-time variation in Chinese cabbage. Collectively, our study provides valuable insights into the genetic basis of spring Chinese cabbage selection and will facilitate the breeding of bolting-resistant varieties by molecular-marker-assisted selection, transgenic or gene editing approaches.
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Affiliation(s)
- Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Bin Zhang
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Pan Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
| | - Honghe Sun
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Gang Zhou
- Biomarker Technologies Corporation, Beijing, China
| | - Yuntong Wang
- Biomarker Technologies Corporation, Beijing, China
| | | | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China.
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China.
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32
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Lo S, Muñoz-Amatriaín M, Boukar O, Herniter I, Cisse N, Guo YN, Roberts PA, Xu S, Fatokun C, Close TJ. Identification of QTL controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp). Sci Rep 2018; 8:6261. [PMID: 29674702 PMCID: PMC5908840 DOI: 10.1038/s41598-018-24349-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/29/2018] [Indexed: 11/08/2022] Open
Abstract
Cowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTL) for these nine traits. Based on annotations of the cowpea reference genome, genes within these regions are reported. Four regions with clusters of QTL were identified, including one on chromosome 8 related to increased organ size. This study provides new knowledge of the genomic regions controlling domestication-related traits in cowpea as well as candidate genes underlying those QTL. This information can help to exploit wild relatives in cowpea breeding programs.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA.
| | - Ousmane Boukar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Ira Herniter
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Ndiaga Cisse
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sècheresse, ISRA/CERAAS, Thies, Senegal
| | - Yi-Ning Guo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Philip A Roberts
- Department of Nematology, University of California Riverside, Riverside, CA, USA
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | | | - Timothy J Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
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Mastretta-Yanes A, Acevedo Gasman F, Burgeff C, Cano Ramírez M, Piñero D, Sarukhán J. An Initiative for the Study and Use of Genetic Diversity of Domesticated Plants and Their Wild Relatives. FRONTIERS IN PLANT SCIENCE 2018; 9:209. [PMID: 29515612 PMCID: PMC5826304 DOI: 10.3389/fpls.2018.00209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 02/05/2018] [Indexed: 05/25/2023]
Abstract
Domestication has been influenced by formal plant breeding since the onset of intensive agriculture and the Green Revolution. Despite providing food security for some regions, intensive agriculture has had substantial detrimental consequences for the environment and does not fulfill smallholder's needs under most developing countries conditions. Therefore, it is necessary to look for alternative plant production techniques, effective for each environmental, socio-cultural, and economic conditions. This is particularly relevant for countries that are megadiverse and major centers of plant domestication and diversification. In this white paper, a Mexico-centered initiative is proposed, with two main objectives: (1) to study, understand, conserve, and sustainably use the genetic diversity of domesticated plants and their wild relatives, as well as the ongoing evolutionary processes that generate and maintain it; and (2) to strengthen food and forestry production in a socially fair and environmentally friendly way. To fulfill these objectives, the initiative focuses on the source of variability available for domestication (genetic diversity and functional genomics), the context in which domestication acts (breeding and production) and one of its main challenges (environmental change). Research on these components can be framed to target and connect both the theoretical understanding of the evolutionary processes, the practical aspects of conservation, and food and forestry production. The target, main challenges, problems to be faced and key research questions are presented for each component, followed by a roadmap for the consolidation of this proposal as a national initiative.
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Affiliation(s)
- Alicia Mastretta-Yanes
- CONACYT – Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Mexico City, Mexico
| | | | - Caroline Burgeff
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Mexico City, Mexico
| | | | - Daniel Piñero
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - José Sarukhán
- Instituto de Ecología, Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Hernández-Terán A, Wegier A, Benítez M, Lira R, Escalante AE. Domesticated, Genetically Engineered, and Wild Plant Relatives Exhibit Unintended Phenotypic Differences: A Comparative Meta-Analysis Profiling Rice, Canola, Maize, Sunflower, and Pumpkin. FRONTIERS IN PLANT SCIENCE 2017; 8:2030. [PMID: 29259610 PMCID: PMC5723393 DOI: 10.3389/fpls.2017.02030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/14/2017] [Indexed: 05/29/2023]
Abstract
Agronomic management of plants is a powerful evolutionary force acting on their populations. The management of cultivated plants is carried out by the traditional process of human selection or plant breeding and, more recently, by the technologies used in genetic engineering (GE). Even though crop modification through GE is aimed at specific traits, it is possible that other non-target traits can be affected by genetic modification due to the complex regulatory processes of plant metabolism and development. In this study, we conducted a meta-analysis profiling the phenotypic consequences of plant breeding and GE, and compared modified cultivars with wild relatives in five crops of global economic and cultural importance: rice, maize, canola, sunflower, and pumpkin. For these five species, we analyzed the literature with documentation of phenotypic traits that are potentially related to fitness for the same species in comparable conditions. The information was analyzed to evaluate whether the different processes of modification had influenced the phenotype in such a way as to cause statistical differences in the state of specific phenotypic traits or grouping of the organisms depending on their genetic origin [wild, domesticated with genetic engineering (domGE), and domesticated without genetic engineering (domNGE)]. In addition, we tested the hypothesis that, given that transgenic plants are a construct designed to impact, in many cases, a single trait of the plant (e.g., lepidopteran resistance), the phenotypic differences between domGE and domNGE would be either less (or inexistent) than between the wild and domesticated relatives (either domGE or domNGE). We conclude that (1) genetic modification (either by selective breeding or GE) can be traced phenotypically when comparing wild relatives with their domesticated relatives (domGE and domNGE) and (2) the existence and the magnitude of the phenotypic differences between domGE and domNGE of the same crop suggest consequences of genetic modification beyond the target trait(s).
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Affiliation(s)
- Alejandra Hernández-Terán
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana Wegier
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rafael Lira
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana E. Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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35
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Chávez-Pesqueira M, Núñez-Farfán J. Domestication and Genetics of Papaya: A Review. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00155] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Guerra-García A, Suárez-Atilano M, Mastretta-Yanes A, Delgado-Salinas A, Piñero D. Domestication Genomics of the Open-Pollinated Scarlet Runner Bean ( Phaseolus coccineus L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1891. [PMID: 29187858 PMCID: PMC5694824 DOI: 10.3389/fpls.2017.01891] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/18/2017] [Indexed: 05/25/2023]
Abstract
The runner bean is a legume species from Mesoamerica closely related to common bean (Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In this work we aim to (1) provide information about the domestication history and domestication events of P. coccineus; (2) examine the distribution and level of genetic diversity in wild and cultivated Mexican populations of this species; and, (3) identify candidate loci to natural and artificial selection. For this, we generated genotyping by sequencing data (42,548 SNPs) from 242 individuals of P. coccineus and the domesticated forms of the closely related species P. vulgaris (20) and P. dumosus (35). Eight genetic clusters were detected, of which half corresponds to wild populations and the rest to domesticated plants. The cultivated populations conform a monophyletic clade, suggesting that only one domestication event occurred in Mexico, and that it took place around populations of the Trans-Mexican Volcanic Belt. No difference between wild and domesticated levels of genetic diversity was detected and effective population sizes are relatively high, supporting a weak genetic bottleneck during domestication. Most populations presented an excess of heterozygotes, probably due to inbreeding depression. One population of P. coccineus subsp. striatus had the greatest excess and seems to be genetically isolated despite being geographically close to other wild populations. Contrasting with previous studies, we did not find evidence of recent gene flow between wild and cultivated populations. Based on outlier detection methods, we identified 24 domestication-related SNPs, 13 related to cultivar diversification and eight under natural selection. Few of these SNPs fell within annotated loci, but the annotated domestication-related SNPs are highly expressed in flowers and pods. Our results contribute to the understanding of the domestication history of P. coccineus, and highlight how the genetic signatures of domestication can be substantially different between closely related species.
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Affiliation(s)
- Azalea Guerra-García
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Marco Suárez-Atilano
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alicia Mastretta-Yanes
- CONACYT-CONABIO, Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Ciudad de México, Mexico
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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37
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Kantar MB, Nashoba AR, Anderson JE, Blackman BK, Rieseberg LH. The Genetics and Genomics of Plant Domestication. Bioscience 2017. [DOI: 10.1093/biosci/bix114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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38
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Branstetter MG, Ješovnik A, Sosa-Calvo J, Lloyd MW, Faircloth BC, Brady SG, Schultz TR. Dry habitats were crucibles of domestication in the evolution of agriculture in ants. Proc Biol Sci 2017; 284:rspb.2017.0095. [PMID: 28404776 PMCID: PMC5394666 DOI: 10.1098/rspb.2017.0095] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/14/2017] [Indexed: 11/12/2022] Open
Abstract
The evolution of ant agriculture, as practised by the fungus-farming 'attine' ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The 'out-of-the-rainforest' hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required. Here, we use phylogenomic data from ultra-conserved element (UCE) loci to reconstruct the evolutionary history of fungus-farming ants, reduce topological uncertainty, and identify the closest non-fungus-growing ant relative. Using the phylogeny we infer the history of attine agricultural systems, habitat preference and biogeography. Our results show that the out-of-the-rainforest hypothesis is correct with regard to the origin of attine ant agriculture; however, contrary to expectation, we find that the transition from lower to higher agriculture is very likely to have occurred in a seasonally dry habitat, inhospitable to the growth of free-living populations of attine fungal cultivars. We suggest that dry habitats favoured the isolation of attine cultivars over the evolutionary time spans necessary for domestication to occur.
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Affiliation(s)
- Michael G Branstetter
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA .,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Ana Ješovnik
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Jeffrey Sosa-Calvo
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Center for Social Insect Research, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael W Lloyd
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Ted R Schultz
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
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39
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Gascuel Q, Diretto G, Monforte AJ, Fortes AM, Granell A. Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape. FRONTIERS IN PLANT SCIENCE 2017; 8:652. [PMID: 28553296 PMCID: PMC5427129 DOI: 10.3389/fpls.2017.00652] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/10/2017] [Indexed: 05/18/2023]
Abstract
Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards. Furthermore, progress has largely been limited to simple agronomic traits easy-to-observe, whereas the vast majority of quality attributes, specifically those relating to flavor and nutrition, are complex and have mostly been neglected. Fortunately, wild germplasm, which is used for resistance against/tolerance of environmental stresses (including pathogens), is still available and harbors significant genetic variation for taste and health-promoting traits. Similarly, heirloom/traditional varieties could be used to identify which genes contribute to flavor and health quality and, at the same time, serve as a good source of the best alleles for organoleptic quality improvement. Grape (Vitis vinifera L.) and tomato (Solanum lycopersicum L.) produce fleshy, berry-type fruits, among the most consumed in the world. Both have undergone important domestication and selection processes, that have dramatically reduced their genetic variability, and strongly standardized fruit traits. Moreover, more and more consumers are asking for sustainable production, incompatible with the wide range of chemical inputs. In the present paper, we review the genetic resources available to tomato/grape breeders, and the recent technological progresses that facilitate the identification of genes/alleles of interest within the natural or generated variability gene pool. These technologies include omics, high-throughput phenotyping/phenomics, and biotech approaches. Our review also covers a range of technologies used to transfer to tomato and grape those alleles considered of interest for fruit quality. These include traditional breeding, TILLING (Targeting Induced Local Lesions in Genomes), genetic engineering, or NPBT (New Plant Breeding Technologies). Altogether, the combined exploitation of genetic variability and innovative biotechnological tools may facilitate breeders to improve fruit quality tacking more into account the consumer standards and the needs to move forward into more sustainable farming practices.
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Affiliation(s)
- Quentin Gascuel
- Laboratory of Plant-Microbe Interactions, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Toulouse UniversityCastanet Tolosan, France
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research CentreRome, Italy
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Universidad Politécnica de ValenciaValencia, Spain
| | - Ana M. Fortes
- Faculdade de Ciências de Lisboa, Instituto de Biossistemas e Ciências Integrativas (BioISI), Universidade de LisboaLisboa, Portugal
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Universidad Politécnica de ValenciaValencia, Spain
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Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S, Vlasova A, Capella-Gutierrez S, Ordaz-Ortiz JJ, Aguilar OM, Vianello-Brondani RP, Santalla M, Delaye L, Gabaldón T, Gepts P, Winkler R, Guigó R, Delgado-Salinas A, Herrera-Estrella A. Genomic history of the origin and domestication of common bean unveils its closest sister species. Genome Biol 2017; 18:60. [PMID: 28356141 PMCID: PMC5370463 DOI: 10.1186/s13059-017-1190-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/07/2017] [Indexed: 11/19/2022] Open
Abstract
Background Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. Results We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. Conclusions We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1190-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - Josaphat M Montero-Vargas
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Soledad Saburido-Álvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - Anna Vlasova
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutierrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José Juan Ordaz-Ortiz
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | | | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, Irapuato, Guanajuato, Mexico
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA, 95616-8780, USA
| | - Robert Winkler
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Roderic Guigó
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico.
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41
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Stetter MG, Müller T, Schmid KJ. Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus
). Mol Ecol 2017; 26:871-886. [DOI: 10.1111/mec.13974] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/09/2016] [Accepted: 12/14/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Markus G. Stetter
- Institute of Plant Breeding, Seed Science and Population Genetics; University of Hohenheim; Fruwirthstraße 21 D-70599 Stuttgart Germany
| | - Thomas Müller
- Institute of Plant Breeding, Seed Science and Population Genetics; University of Hohenheim; Fruwirthstraße 21 D-70599 Stuttgart Germany
| | - Karl J. Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics; University of Hohenheim; Fruwirthstraße 21 D-70599 Stuttgart Germany
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He C, Fu J, Zhang J, Li Y, Zheng J, Zhang H, Yang X, Wang J, Wang G. A Gene-Oriented Haplotype Comparison Reveals Recently Selected Genomic Regions in Temperate and Tropical Maize Germplasm. PLoS One 2017; 12:e0169806. [PMID: 28099470 PMCID: PMC5242465 DOI: 10.1371/journal.pone.0169806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/21/2016] [Indexed: 11/19/2022] Open
Abstract
The extensive genetic variation present in maize (Zea mays) germplasm makes it possible to detect signatures of positive artificial selection that occurred during temperate and tropical maize improvement. Here we report an analysis of 532,815 polymorphisms from a maize association panel consisting of 368 diverse temperate and tropical inbred lines. We developed a gene-oriented approach adapting exonic polymorphisms to identify recently selected alleles by comparing haplotypes across the maize genome. This analysis revealed evidence of selection for more than 1100 genomic regions during recent improvement, and included regulatory genes and key genes with visible mutant phenotypes. We find that selected candidate target genes in temperate maize are enriched in biosynthetic processes, and further examination of these candidates highlights two cases, sucrose flux and oil storage, in which multiple genes in a common pathway can be cooperatively selected. Finally, based on available parallel gene expression data, we hypothesize that some genes were selected for regulatory variations, resulting in altered gene expression.
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Affiliation(s)
- Cheng He
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zhang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohong Yang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Jianhua Wang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
- * E-mail: (GW); (JW)
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (GW); (JW)
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Macko-Podgórni A, Machaj G, Stelmach K, Senalik D, Grzebelus E, Iorizzo M, Simon PW, Grzebelus D. Characterization of a Genomic Region under Selection in Cultivated Carrot ( Daucus carota subsp. sativus) Reveals a Candidate Domestication Gene. FRONTIERS IN PLANT SCIENCE 2017; 8:12. [PMID: 28149306 PMCID: PMC5241283 DOI: 10.3389/fpls.2017.00012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/04/2017] [Indexed: 05/11/2023]
Abstract
Carrot is one of the most important vegetables worldwide, owing to its capability to develop fleshy, highly nutritious storage roots. It was domesticated ca. 1,100 years ago in Central Asia. No systematic knowledge about the molecular mechanisms involved in the domestication syndrome in carrot are available, however, the ability to form a storage root is undoubtedly the essential transition from the wild Daucus carota to the cultivated carrot. Here, we expand on the results of a previous study which identified a polymorphism showing a significant signature for selection upon domestication. We mapped the region under selection to the distal portion of the long arm of carrot chromosome 2, confirmed that it had been selected, as reflected in both the lower nucleotide diversity in the cultivated gene pool, as compared to the wild (πw/πc = 7.4 vs. 1.06 for the whole genome), and the high FST (0.52 vs. 0.12 for the whole genome). We delimited the region to ca. 37 kb in length and identified a candidate domestication syndrome gene carrying three non-synonymous single nucleotide polymorphisms and one indel systematically differentiating the wild and the cultivated accessions. This gene, DcAHLc1, belongs to the AT-hook motif nuclear localized (AHL) family of plant regulatory genes which are involved in the regulation of organ development, including root tissue patterning. AHL genes work through direct interactions with other AHL family proteins and a range of other proteins that require intercellular protein movement. Based on QTL data on root thickening we speculate that DcAHLc1 might be involved in the development of the carrot storage root, as the localization of the gene overlapped with one of the QTLs. According to haplotype information we propose that the 'cultivated' variant of DcAHLc1 has been selected from wild Central Asian carrot populations upon domestication and it is highly predominant in the western cultivated carrot gene pool. However, some primitive eastern landraces and the derived B7262 purple inbred line still carry the 'wild' variant, reflecting a likely complexity of the genetic determination of the formation of carrot storage roots.
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Affiliation(s)
- Alicja Macko-Podgórni
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
| | - Gabriela Machaj
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
| | - Katarzyna Stelmach
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
| | - Douglas Senalik
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Department of Horticulture, University of Wisconsin–Madison, MadisonWI, USA
| | - Ewa Grzebelus
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
| | - Massimo Iorizzo
- Plants for Human Health Institute, Department of Horticultural Science, North Carolina State University, KannapolisNC, USA
| | - Philipp W. Simon
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Department of Horticulture, University of Wisconsin–Madison, MadisonWI, USA
| | - Dariusz Grzebelus
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in KrakowKrakow, Poland
- *Correspondence: Dariusz Grzebelus,
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Cheng F, Sun R, Hou X, Zheng H, Zhang F, Zhang Y, Liu B, Liang J, Zhuang M, Liu Y, Liu D, Wang X, Li P, Liu Y, Lin K, Bucher J, Zhang N, Wang Y, Wang H, Deng J, Liao Y, Wei K, Zhang X, Fu L, Hu Y, Liu J, Cai C, Zhang S, Zhang S, Li F, Zhang H, Zhang J, Guo N, Liu Z, Liu J, Sun C, Ma Y, Zhang H, Cui Y, Freeling MR, Borm T, Bonnema G, Wu J, Wang X. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet 2016; 48:1218-24. [PMID: 27526322 DOI: 10.1038/ng.3634] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 07/01/2016] [Indexed: 12/21/2022]
Abstract
Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.
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Affiliation(s)
- Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang, Nanjing, China
| | | | - Fenglan Zhang
- Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing Vegetable Research Center (BVRC), Beijing, China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Bo Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yunxia Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Dongyuan Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Xiaobo Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Pingxia Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yumei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Ke Lin
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Johan Bucher
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Ningwen Zhang
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Yan Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Hui Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jie Deng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yongcui Liao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Keyun Wei
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Xueming Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Lixia Fu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yunyan Hu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jisheng Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Chengcheng Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jifang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Ning Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Zhiyuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jin Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Chao Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yuan Ma
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Haijiao Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yang Cui
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Micheal R Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkley, California, USA
| | - Theo Borm
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Guusje Bonnema
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.,Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
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Beleggia R, Rau D, Laidò G, Platani C, Nigro F, Fragasso M, De Vita P, Scossa F, Fernie AR, Nikoloski Z, Papa R. Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels. Mol Biol Evol 2016; 33:1740-53. [PMID: 27189559 PMCID: PMC4915355 DOI: 10.1093/molbev/msw050] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Domestication and breeding have influenced the genetic structure of plant populations due to selection for adaptation from natural habitats to agro-ecosystems. Here, we investigate the effects of selection on the contents of 51 primary kernel metabolites and their relationships in three Triticum turgidum L. subspecies (i.e., wild emmer, emmer, durum wheat) that represent the major steps of tetraploid wheat domestication. We present a methodological pipeline to identify the signature of selection for molecular phenotypic traits (e.g., metabolites and transcripts). Following the approach, we show that a reduction in unsaturated fatty acids was associated with selection during domestication of emmer (primary domestication). We also show that changes in the amino acid content due to selection mark the domestication of durum wheat (secondary domestication). These effects were found to be partially independent of the associations that unsaturated fatty acids and amino acids have with other domestication-related kernel traits. Changes in contents of metabolites were also highlighted by alterations in the metabolic correlation networks, indicating wide metabolic restructuring due to domestication. Finally, evidence is provided that wild and exotic germplasm can have a relevant role for improvement of wheat quality and nutritional traits.
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Affiliation(s)
- Romina Beleggia
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Giovanni Laidò
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Cristiano Platani
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy Consiglio per la ricerca in agricoltura e l'analisi dell' economia agraria - Unità di Ricerca per l'Orticoltura (CREA-ORA), Monsampolo del Tronto (AP), Italy
| | - Franca Nigro
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Mariagiovanna Fragasso
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Pasquale De Vita
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Federico Scossa
- Consiglio per la ricerca in agricoltura e l'analisi dell' economia agraria, Centro di Ricerca per la Frutticoltura (CREA-FRU), Roma, Italy
| | - Alisdair R Fernie
- Central Metabolism Group, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Roberto Papa
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy Dipartimento di Scienze Agrarie, Alimentari e Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
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Swinnen G, Goossens A, Pauwels L. Lessons from Domestication: Targeting Cis-Regulatory Elements for Crop Improvement. TRENDS IN PLANT SCIENCE 2016; 21:506-515. [PMID: 26876195 DOI: 10.1016/j.tplants.2016.01.014] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/21/2015] [Accepted: 01/12/2016] [Indexed: 05/20/2023]
Abstract
Domestication of wild plant species has provided us with crops that serve our human nutritional needs. Advanced DNA sequencing has propelled the unveiling of underlying genetic changes associated with domestication. Interestingly, many changes reside in cis-regulatory elements (CREs) that control the expression of an unmodified coding sequence. Sequence variation in CREs can impact gene expression levels, but also developmental timing and tissue specificity of expression. When genes are involved in multiple pathways or active in several organs and developmental stages CRE modifications are favored in contrast to mutations in coding regions, due to the lack of detrimental pleiotropic effects. Therefore, learning from domestication, we propose that CREs are interesting targets for genome editing to create new alleles for plant breeding.
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Affiliation(s)
- Gwen Swinnen
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium.
| | - Laurens Pauwels
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium.
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Valdisser PAMR, Pappas GJ, de Menezes IPP, Müller BSF, Pereira WJ, Narciso MG, Brondani C, Souza TLPO, Borba TCO, Vianello RP. SNP discovery in common bean by restriction-associated DNA (RAD) sequencing for genetic diversity and population structure analysis. Mol Genet Genomics 2016; 291:1277-91. [PMID: 26932372 DOI: 10.1007/s00438-016-1182-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 02/12/2016] [Indexed: 11/28/2022]
Abstract
Researchers have made great advances into the development and application of genomic approaches for common beans, creating opportunities to driving more real and applicable strategies for sustainable management of the genetic resource towards plant breeding. This work provides useful polymorphic single-nucleotide polymorphisms (SNPs) for high-throughput common bean genotyping developed by RAD (restriction site-associated DNA) sequencing. The RAD tags were generated from DNA pooled from 12 common bean genotypes, including breeding lines of different gene pools and market classes. The aligned sequences identified 23,748 putative RAD-SNPs, of which 3357 were adequate for genotyping; 1032 RAD-SNPs with the highest ADT (assay design tool) score are presented in this article. The RAD-SNPs were structurally annotated in different coding (47.00 %) and non-coding (53.00 %) sequence components of genes. A subset of 384 RAD-SNPs with broad genome distribution was used to genotype a diverse panel of 95 common bean germplasms and revealed a successful amplification rate of 96.6 %, showing 73 % of polymorphic SNPs within the Andean group and 83 % in the Mesoamerican group. A slightly increased He (0.161, n = 21) value was estimated for the Andean gene pool, compared to the Mesoamerican group (0.156, n = 74). For the linkage disequilibrium (LD) analysis, from a group of 580 SNPs (289 RAD-SNPs and 291 BARC-SNPs) genotyped for the same set of genotypes, 70.2 % were in LD, decreasing to 0.10 %in the Andean group and 0.77 % in the Mesoamerican group. Haplotype patterns spanning 310 Mb of the genome (60 %) were characterized in samples from different origins. However, the haplotype frameworks were under-represented for the Andean (7.85 %) and Mesoamerican (5.55 %) gene pools separately. In conclusion, RAD sequencing allowed the discovery of hundreds of useful SNPs for broad genetic analysis of common bean germplasm. From now, this approach provides an excellent panel of molecular tools for whole genome analysis, allowing integrating and better exploring the common bean breeding practices.
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Affiliation(s)
| | - Georgios J Pappas
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Universidade de Brasília (UnB), Brasilia, DF, Brazil
| | - Ivandilson P P de Menezes
- Laboratório de Genética e Biologia Molecular, Departamento de Biologia, Instituto Federal Goiano (IF Goiano), Urutaí, GO, Brazil
| | - Bárbara S F Müller
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasilia, DF, Brazil
| | - Wendell J Pereira
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
| | - Marcelo G Narciso
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil
| | - Claudio Brondani
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil
| | - Thiago L P O Souza
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil
| | - Tereza C O Borba
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil
| | - Rosana P Vianello
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil.
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Gaut BS, Díez CM, Morrell PL. Genomics and the Contrasting Dynamics of Annual and Perennial Domestication. Trends Genet 2015; 31:709-719. [PMID: 26603610 DOI: 10.1016/j.tig.2015.10.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/08/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
Abstract
Plant domestication modifies a wild species genetically for human use. Among thousands of domesticated plants, a major distinction is the difference between annual and perennial life cycles. The domestication of perennials is expected to follow different processes than annuals, with distinct genetic outcomes. Here we examine domestication from a population genetics perspective, with a focus on three issues: genetic bottlenecks during domestication, introgression as a source of local adaptation, and genetic load. These three issues have been studied nominally in major annual crops but even less extensively in perennials. Here we highlight lessons from annual plants, motivations to study these issues in perennial plants, and new approaches that may lead to further progress.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA.
| | - Concepción M Díez
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3, Edificio C4, Campus de Rabanales, 14014 Córdoba, Spain
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
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Zou H, Tzarfati R, Hübner S, Krugman T, Fahima T, Abbo S, Saranga Y, Korol AB. Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars. BMC Genomics 2015; 16:777. [PMID: 26462652 PMCID: PMC4603339 DOI: 10.1186/s12864-015-1996-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/03/2015] [Indexed: 12/02/2022] Open
Abstract
Background Wheat domestication is considered as one of the most important events in the development of human civilization. Wheat spikelets have undergone significant changes during evolution under domestication, resulting in soft glumes and larger kernels that are released easily upon threshing. Our main goal was to explore changes in transcriptome expression in glumes that accompanied wheat evolution under domestication. Methods A total of six tetraploid wheat accessions were selected for transcriptome profiling based on their rachis brittleness and glumes toughness. RNA pools from glumes of the central spikelet at heading time were used to construct cDNA libraries for sequencing. The trimmed reads from each library were separately aligned to the reference sub-genomes A and B, which were extracted from wheat survey sequence. Differentially expression analysis and functional annotation were performed between wild and domesticated wheat, to identity candidate genes associated with evolution under domestication. Selected candidate genes were validated using real time PCR. Results Transcriptome profiles of wild emmer wheat, wheat landraces, and wheat cultivars were compared using next generation sequencing (RNA-seq). We have found a total of 194,893 transcripts, of which 73,150 were shared between wild, landraces, and cultivars. From 781 differentially expressed genes (DEGs), 336 were down-regulated and 445 were up-regulated in the domesticated compared to wild wheat genotypes. Gene Ontology (GO) annotation assigned 293 DEGs (37.5 %) to GO term groups, of which 134 (17.1 %) were down-regulated and 159 (20.4 %) up-regulated in the domesticated wheat. Some of the down-regulated DEGs in domesticated wheat are related to the biosynthetic pathways that eventually define the mechanical strength of the glumes, such as cell wall, lignin, pectin and wax biosynthesis. The reduction in gene expression of such genes, may explain the softness of the glumes in the domesticated forms. In addition, we have identified genes involved in nutrient remobilization that may affect grain size and other agronomic traits evolved under domestication. Conclusions The comparison of RNA-seq profiles between glumes of wheat groups differing in glumes toughness and rachis brittleness revealed a few DEGs that may be involved in glumes toughness and nutrient remobilization. These genes may be involved in processes of wheat improvement under domestication. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1996-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongda Zou
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Raanan Tzarfati
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Sariel Hübner
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Tamar Krugman
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Shahal Abbo
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Yehoshua Saranga
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Abraham B Korol
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
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