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Landis JB, Guercio AM, Brown KE, Fiscus CJ, Morrell PL, Koenig D. Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley. Science 2024; 385:eadl0038. [PMID: 38991084 DOI: 10.1126/science.adl0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 05/21/2024] [Indexed: 07/13/2024]
Abstract
Direct observation is central to our understanding of adaptation, but evolution is rarely documented in a large, multicellular organism for more than a few generations. In this study, we observed evolution across a century-scale competition experiment, barley composite cross II (CCII). CCII was founded in 1929 in Davis, California, with thousands of genotypes, but we found that natural selection has massively reduced genetic diversity, leading to a single lineage constituting most of the population by generation 50. Selection favored alleles originating from climates similar to that of Davis and targeted loci contributing to reproductive development, including the barley diversification loci Vrs1, HvCEN, Ppd-H1, and Vrn-H2. Our findings point to selection as the predominant force shaping genomic variation in one of the world's oldest biological experiments.
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Affiliation(s)
- Jacob B Landis
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Angelica M Guercio
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Keely E Brown
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Christopher J Fiscus
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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2
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Omondi EO, Lin CY, Huang SM, Liao CA, Lin YP, Oliva R, van Zonneveld M. Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplants. Ecol Evol 2024; 14:e11662. [PMID: 38983700 PMCID: PMC11232056 DOI: 10.1002/ece3.11662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024] Open
Abstract
Crop wild relatives (CWR) provide a valuable resource for improving crops. They possess desirable traits that confer resilience to various environmental stresses. To fully utilize crop wild relatives in breeding and conservation programs, it is important to understand the genetic basis of their adaptation. Landscape genomics associates environments with genomic variation and allows for examining the genetic basis of adaptation. Our study examined the differences in allele frequency of 15,416 single nucleotide polymorphisms (SNPs) generated through genotyping by sequencing approach among 153 accessions of 15 wild eggplant relatives and two cultivated species from Africa, the principal hotspot of these wild relatives. We also explored the correlation between these variations and the bioclimatic and soil conditions at their collection sites, providing a comprehensive understanding of the genetic signals of environmental adaptation in African wild eggplant. Redundancy analysis (RDA) results showed that the environmental variation explained 6% while the geographical distances among the collection sites explained 15% of the genomic variation in the eggplant wild relative populations when controlling for population structure. Our findings indicate that even though environmental factors are not the main driver of selection in eggplant wild relatives, it is influential in shaping the genomic variation over time. The selected environmental variables and candidate SNPs effectively revealed grouping patterns according to the environmental characteristics of sampling sites. Using four genotype-environment association methods, we detected 396 candidate SNPs (2.5% of the initial SNPs) associated with eight environmental factors. Some of these SNPs signal genes involved in pathways that help adapt to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. These candidate SNPs will be useful for marker-assisted improvement and characterizing the germplasm of this crop for developing climate-resilient eggplant varieties. The study provides a model for applying landscape genomics to other crops' wild relatives.
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Affiliation(s)
- Emmanuel O Omondi
- Genetic Resources and Seed Unit World Vegetable Center Tainan Taiwan
| | - Chen-Yu Lin
- Biotechnology, World Vegetable Center Tainan Taiwan
| | | | - Cheng-An Liao
- Department of Horticulture National Taiwan University Taipei Taiwan
| | - Ya-Ping Lin
- Biotechnology, World Vegetable Center Tainan Taiwan
| | - Ricardo Oliva
- Plant Pathology World Vegetable Center Tainan Taiwan
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3
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Chen T, Xu J, Wang L, Wang H, You E, Deng C, Bian H, Shen Y. Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau. Heredity (Edinb) 2023; 131:316-326. [PMID: 37935814 PMCID: PMC10673939 DOI: 10.1038/s41437-023-00647-0] [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: 12/05/2022] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 11/09/2023] Open
Abstract
Understanding the local adaptation of crops has long been a concern of evolutionary biologists and molecular ecologists. Identifying the adaptive genetic variability in the genome is crucial not only to provide insights into the genetic mechanism of local adaptation but also to explore the adaptation potential of crops. This study aimed to identify the climatic drivers of naked barley landraces and putative adaptive loci driving local adaptation on the Qinghai-Tibetan Plateau (QTP). To this end, a total of 157 diverse naked barley accessions were genotyped using the genotyping-by-sequencing approach, which yielded 3123 high-quality SNPs for population structure analysis and partial redundancy analysis, and 37,636 SNPs for outlier analysis. The population structure analysis indicated that naked barley landraces could be divided into four groups. We found that the genomic diversity of naked barley landraces could be partly traced back to the geographical and environmental diversity of the landscape. In total, 136 signatures associated with temperature, precipitation, and ultraviolet radiation were identified, of which 13 had pleiotropic effects. We mapped 447 genes, including a known gene HvSs1. Some genes involved in cold stress and regulation of flowering time were detected near eight signatures. Taken together, these results highlight the existence of putative adaptive loci in naked barley on QTP and thus improve our current understanding of the genetic basis of local adaptation.
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Affiliation(s)
- Tongrui Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinqing Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - Handong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - En You
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Deng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Bian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhu Shen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China.
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4
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Bethke G, Huang Y, Hensel G, Heinen S, Liu C, Wyant SR, Li X, Quin MB, McCormick S, Morrell PL, Dong Y, Kumlehn J, Salvi S, Berthiller F, Muehlbauer GJ. UDP-glucosyltransferase HvUGT13248 confers type II resistance to Fusarium graminearum in barley. PLANT PHYSIOLOGY 2023; 193:2691-2710. [PMID: 37610244 DOI: 10.1093/plphys/kiad467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
Fusarium head blight (FHB) of barley (Hordeum vulgare) causes yield losses and accumulation of trichothecene mycotoxins (e.g. deoxynivalenol [DON]) in grains. Glucosylation of DON to the nontoxic DON-3-O-glucoside (D3G) is catalyzed by UDP-glucosyltransferases (UGTs), such as barley UGT13248. We explored the natural diversity of UGT13248 in 496 barley accessions and showed that all carried potential functional alleles of UGT13248, as no genotypes showed strongly increased seedling sensitivity to DON. From a TILLING population, we identified 2 mutant alleles (T368I and H369Y) that, based on protein modeling, likely affect the UDP-glucose binding of UGT13248. In DON feeding experiments, DON-to-D3G conversion was strongly reduced in spikes of these mutants compared to controls, and plants overexpressing UGT13248 showed increased resistance to DON and increased DON-to-D3G conversion. Moreover, field-grown plants carrying the T368I or H369Y mutations inoculated with Fusarium graminearum showed increased FHB disease severity and reduced D3G production. Barley is generally considered to have type II resistance that limits the spread of F. graminearum from the infected spikelet to adjacent spikelets. Point inoculation experiments with F. graminearum showed increased infection spread in T368I and H369Y across the spike compared to wild type, while overexpression plants showed decreased spread of FHB symptoms. Confocal microscopy revealed that F. graminearum spread to distant rachis nodes in T368I and H369Y mutants but was arrested at the rachis node of the inoculated spikelet in wild-type plants. Taken together, our data reveal that UGT13248 confers type II resistance to FHB in barley via conjugation of DON to D3G.
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Affiliation(s)
- Gerit Bethke
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yadong Huang
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Goetz Hensel
- Department of Physiology and Cell Biology, Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Shane Heinen
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Skylar R Wyant
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Maureen B Quin
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Susan McCormick
- Mycotoxin Prevention and Applied Microbiology Research, USDA-ARS NCAUR, Peoria, IL 61604, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jochen Kumlehn
- Department of Physiology and Cell Biology, Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40126, Italy
| | - Franz Berthiller
- Department of Agrobiotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln 3430, Austria
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
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5
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Bedford JA, Carine M, Chapman MA. Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis. G3 (BETHESDA, MD.) 2023; 13:jkad194. [PMID: 37619981 PMCID: PMC10542315 DOI: 10.1093/g3journal/jkad194] [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: 07/19/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.
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Affiliation(s)
- James A Bedford
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark Carine
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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Wang DR, Kantar MB, Murugaiyan V, Neyhart J. Where the wild things are: genetic associations of environmental adaptation in the Oryza rufipogon species complex. G3 (BETHESDA, MD.) 2023; 13:jkad128. [PMID: 37293846 PMCID: PMC10411557 DOI: 10.1093/g3journal/jkad128] [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: 03/01/2023] [Revised: 05/02/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023]
Abstract
Crop wild relatives host unique adaptation strategies that enable them to thrive across a wide range of habitats. As pressures from a changing climate mount, a more complete understanding of the genetic variation that underlies this adaptation could enable broader utilization of wild materials for crop improvement. Here, we carry out environmental association analyses (EAA) in the Oryza rufipogon species complex (ORSC), the wild progenitor of cultivated Asian rice, to identify genomic regions associated with environmental adaptation characterized by variation in bioclimatic and soil variables. We further examine regions for colocalizations with phenotypic associations within the same collection. EAA results indicate that significant regions tend to associate with single environmental variables, although 2 significant loci on chromosomes 3 and 5 are detected as common across multiple variable types (i.e. precipitation, temperature, and/or soil). Distributions of allele frequencies at significant loci across subpopulations of cultivated Oryza sativa indicate that, in some cases, adaptive variation may already be present among cultivars, although evaluation in cultivated populations is needed to empirically test this. This work has implications for the potential utility of wild genetic resources in pre-breeding efforts for rice improvement.
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Affiliation(s)
- Diane R Wang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Michael B Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Manoa, Honolulu, HI 96822, USA
| | - Varunseelan Murugaiyan
- Rice Breeding Platform, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila 1301, Philippines
| | - Jeffrey Neyhart
- USDA-ARS, Genetic Improvement for Fruits and Vegetables Laboratory, Chatsworth, NJ 08019, USA
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7
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Neyhart JL, Kantar MB, Zalapa J, Vorsa N. Genomic-environmental associations in wild cranberry (Vaccinium macrocarpon Ait.). G3 (BETHESDA, MD.) 2022; 12:jkac203. [PMID: 35944211 PMCID: PMC9526045 DOI: 10.1093/g3journal/jkac203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/01/2022] [Indexed: 06/01/2023]
Abstract
Understanding the genetic basis of local adaptation in natural plant populations, particularly crop wild relatives, may be highly useful for plant breeding. By characterizing genetic variation for adaptation to potentially stressful environmental conditions, breeders can make targeted use of crop wild relatives to develop cultivars for novel or changing environments. This is especially appealing for improving long-lived woody perennial crops such as the American cranberry (Vaccinium macrocarpon Ait.), the cultivation of which is challenged by biotic and abiotic stresses. In this study, we used environmental association analyses in a collection of 111 wild cranberry accessions to identify potentially adaptive genomic regions for a range of bioclimatic and soil conditions. We detected 126 significant associations between SNP marker loci and environmental variables describing temperature, precipitation, and soil attributes. Many of these markers tagged genes with functional annotations strongly suggesting a role in adaptation to biotic or abiotic conditions. Despite relatively low genetic variation in cranberry, our results suggest that local adaptation to divergent environments is indeed present, and the identification of potentially adaptive genetic variation may enable a selective use of this germplasm for breeding more stress-tolerant cultivars.
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Affiliation(s)
- Jeffrey L Neyhart
- USDA, Agricultural Research Service, Genetic Improvement for Fruits & Vegetables Laboratory, Chatsworth, NJ 08019, USA
| | - Michael B Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Juan Zalapa
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
- Department of Horticulture, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Nicholi Vorsa
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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Gómez-Espejo AL, Sansaloni CP, Burgueño J, Toledo FH, Benavides-Mendoza A, Reyes-Valdés MH. Worldwide Selection Footprints for Drought and Heat in Bread Wheat (Triticum aestivum L.). PLANTS 2022; 11:plants11172289. [PMID: 36079671 PMCID: PMC9460392 DOI: 10.3390/plants11172289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/18/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022]
Abstract
Genome–environment Associations (GEA) or Environmental Genome-Wide Association scans (EnvGWAS) have been poorly applied for studying the genomics of adaptive traits in bread wheat landraces (Triticum aestivum L.). We analyzed 990 landraces and seven climatic variables (mean temperature, maximum temperature, precipitation, precipitation seasonality, heat index of mean temperature, heat index of maximum temperature, and drought index) in GEA using the FarmCPU approach with GAPIT. Historical temperature and precipitation values were obtained as monthly averages from 1970 to 2000. Based on 26,064 high-quality SNP loci, landraces were classified into ten subpopulations exhibiting high genetic differentiation. The GEA identified 59 SNPs and nearly 89 protein-encoding genes involved in the response processes to abiotic stress. Genes related to biosynthesis and signaling are mainly mediated by auxins, abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and jasmonates (JA), which are known to operate together in modulation responses to heat stress and drought in plants. In addition, we identified some proteins associated with the response and tolerance to stress by high temperatures, water deficit, and cell wall functions. The results provide candidate regions for selection aimed to improve drought and heat tolerance in bread wheat and provide insights into the genetic mechanisms involved in adaptation to extreme environments.
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Affiliation(s)
- Ana L. Gómez-Espejo
- Programa de Doctorado en Recursos Fitogenéticos para Zonas Áridas, Universidad Autónoma Agraria Antonio Narro (UAAAN), Saltillo 25315, Mexico or
| | | | - Juan Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco 56237, Mexico
| | - Fernando H. Toledo
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco 56237, Mexico
| | - Adalberto Benavides-Mendoza
- Programa de Doctorado en Recursos Fitogenéticos para Zonas Áridas, Universidad Autónoma Agraria Antonio Narro (UAAAN), Saltillo 25315, Mexico or
| | - M. Humberto Reyes-Valdés
- Programa de Doctorado en Recursos Fitogenéticos para Zonas Áridas, Universidad Autónoma Agraria Antonio Narro (UAAAN), Saltillo 25315, Mexico or
- Correspondence:
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9
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Chen Y, Schreiber M, Bayer MM, Dawson IK, Hedley PE, Lei L, Akhunova A, Liu C, Smith KP, Fay JC, Muehlbauer GJ, Steffenson BJ, Morrell PL, Waugh R, Russell JR. The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1580-1594. [PMID: 35834607 PMCID: PMC9546296 DOI: 10.1111/tpj.15908] [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: 04/14/2022] [Revised: 06/30/2022] [Accepted: 07/13/2022] [Indexed: 05/17/2023]
Abstract
The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.
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Affiliation(s)
- Yun‐Yu Chen
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Fios GenomicsBioQuarter, 13 Little France RdEdinburghEH16 4UXUK
| | - Miriam Schreiber
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences, School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | | | - Ian K. Dawson
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Scotland's Rural College, Kings BuildingsWest Mains RdEdinburghEH9 3JGUK
| | | | - Li Lei
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Alina Akhunova
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
- Department of Plant PathologyKansas State UniversityThrockmorton HallManhattanKS66506USA
| | - Chaochih Liu
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Kevin P. Smith
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Justin C. Fay
- Department of BiologyUniversity of Rochester319 HutchisonRochesterNY14627USA
| | - Gary J. Muehlbauer
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Brian J. Steffenson
- Department of Plant PathologyUniversity of Minnesota495 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Peter L. Morrell
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Robbie Waugh
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences, School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
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10
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Cortés AJ, López-Hernández F, Blair MW. Genome–Environment Associations, an Innovative Tool for Studying Heritable Evolutionary Adaptation in Orphan Crops and Wild Relatives. Front Genet 2022; 13:910386. [PMID: 35991553 PMCID: PMC9389289 DOI: 10.3389/fgene.2022.910386] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources of adaptation from landraces, crop wild relatives, and orphan crops is a key prerequisite to accelerate genetic gain of abiotic stress tolerance in annual crops such as legumes and cereals, many of which are still orphan species despite advances in major row crops. Here, we review a novel, interdisciplinary approach to combine ecological climate data with evolutionary genomics under the paradigm of a new field of study: genome–environment associations (GEAs). We first exemplify how GEA utilizes in situ georeferencing from genotypically characterized, gene bank accessions to pinpoint genomic signatures of natural selection. We later discuss the necessity to update the current GEA models to predict both regional- and local- or micro-habitat–based adaptation with mechanistic ecophysiological climate indices and cutting-edge GWAS-type genetic association models. Furthermore, to account for polygenic evolutionary adaptation, we encourage the community to start gathering genomic estimated adaptive values (GEAVs) for genomic prediction (GP) and multi-dimensional machine learning (ML) models. The latter two should ideally be weighted by de novo GWAS-based GEA estimates and optimized for a scalable marker subset. We end the review by envisioning avenues to make adaptation inferences more robust through the merging of high-resolution data sources, such as environmental remote sensing and summary statistics of the genomic site frequency spectrum, with the epigenetic molecular functionality responsible for plastic inheritance in the wild. Ultimately, we believe that coupling evolutionary adaptive predictions with innovations in ecological genomics such as GEA will help capture hidden genetic adaptations to abiotic stresses based on crop germplasm resources to assist responses to climate change. “I shall endeavor to find out how nature’s forces act upon one another, and in what manner the geographic environment exerts its influence on animals and plants. In short, I must find out about the harmony in nature” Alexander von Humboldt—Letter to Karl Freiesleben, June 1799.
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Affiliation(s)
- Andrés J. Cortés
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
- *Correspondence: Andrés J. Cortés, ; Matthew W. Blair,
| | - Felipe López-Hernández
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Matthew W. Blair
- Department of Agricultural & Environmental Sciences, Tennessee State University, Nashville, TN, United States
- *Correspondence: Andrés J. Cortés, ; Matthew W. Blair,
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11
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Sheppard EC, Martin CA, Armstrong C, González-Quevedo C, Illera JC, Suh A, Spurgin LG, Richardson DS. Genomic associations with poxvirus across divergent island populations in Berthelot's pipit. Mol Ecol 2022; 31:3154-3173. [PMID: 35395699 PMCID: PMC9321574 DOI: 10.1111/mec.16461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/04/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022]
Abstract
Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot's pipit (Anthus berthelotii) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses indicates that pathogen-mediated selection may play a role in shaping genomic variation among relatively recently colonised island bird populations and highlights the utility of genotype-environment associations for identifying candidate genes potentially involved in host-pathogen interactions.
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Affiliation(s)
- Eleanor C Sheppard
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Claire Armstrong
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Catalina González-Quevedo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.,Grupo Ecología y Evolución de Vertebrados, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Campus of Mieres, Research Building, 5th Floor, c/ Gonzalo Gutiérrez Quirós, s/n, 33600 Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.,Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
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12
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Borrego-Benjumea A, Carter A, Zhu M, Tucker JR, Zhou M, Badea A. Genome-Wide Association Study of Waterlogging Tolerance in Barley ( Hordeum vulgare L.) Under Controlled Field Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:711654. [PMID: 34512694 PMCID: PMC8427447 DOI: 10.3389/fpls.2021.711654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/21/2021] [Indexed: 06/01/2023]
Abstract
Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8-11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.
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Affiliation(s)
- Ana Borrego-Benjumea
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Adam Carter
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Min Zhu
- College of Agriculture, Yangzhou University, Yangzhou, China
| | - James R. Tucker
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Ana Badea
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
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13
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Fernández-Calleja M, Casas AM, Igartua E. Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1867-1897. [PMID: 33969431 PMCID: PMC8263424 DOI: 10.1007/s00122-021-03824-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/24/2021] [Indexed: 05/10/2023]
Abstract
This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop.
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Affiliation(s)
- Miriam Fernández-Calleja
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ana M Casas
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain.
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14
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Hernandez J, Meints B, Hayes P. Introgression Breeding in Barley: Perspectives and Case Studies. FRONTIERS IN PLANT SCIENCE 2020; 11:761. [PMID: 32595671 PMCID: PMC7303309 DOI: 10.3389/fpls.2020.00761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/13/2020] [Indexed: 05/04/2023]
Abstract
Changing production scenarios resulting from unstable climatic conditions are challenging crop improvement efforts. A deeper and more practical understanding of plant genetic resources is necessary if these assets are to be used effectively in developing improved varieties. In general, current varieties and potential varieties have a narrow genetic base, making them prone to suffer the consequences of new and different abiotic and biotic stresses that can reduce crop yield and quality. The deployment of genomic technologies and sophisticated statistical analysis procedures has generated a dramatic change in the way we characterize and access genetic diversity in crop plants, including barley. Various mapping strategies can be used to identify the genetic variants that lead to target phenotypes and these variants can be assigned coordinates in reference genomes. In this way, new genes and/or new alleles at known loci present in wild ancestors, germplasm accessions, land races, and un-adapted introductions can be located and targeted for introgression. In principle, the introgression process can now be streamlined and linkage drag reduced. In this review, we present an overview of (1) past and current efforts to identify diversity that can be tapped to improve barley yield and quality, and (2) case studies of our efforts to introgress resistance to stripe and stem rust from un-adapted germplasm. We conclude with a description of a modified Nested Association Mapping (NAM) population strategy that we are implementing for the development of multi-use naked barley for organic systems and share perspectives on the use of genome editing in introgression breeding.
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Affiliation(s)
- Javier Hernandez
- Department Crop and Soil Science, Oregon State University, Corvallis, OR, United States
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15
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Kono TJY, Liu C, Vonderharr EE, Koenig D, Fay JC, Smith KP, Morrell PL. The Fate of Deleterious Variants in a Barley Genomic Prediction Population. Genetics 2019; 213:1531-1544. [PMID: 31653677 PMCID: PMC6893365 DOI: 10.1534/genetics.119.302733] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Targeted identification and purging of deleterious genetic variants has been proposed as a novel approach to animal and plant breeding. This strategy is motivated, in part, by the observation that demographic events and strong selection associated with cultivated species pose a "cost of domestication." This includes an increase in the proportion of genetic variants that are likely to reduce fitness. Recent advances in DNA resequencing and sequence constraint-based approaches to predict the functional impact of a mutation permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley lines, we identified 3855 dSNPs among 497,754 total SNPs. We generated whole-genome resequencing data of Hordeum murinum ssp. glaucum as a phylogenetic outgroup to polarize SNPs as ancestral vs. derived. We also observed a higher proportion of dSNPs per synonymous SNPs (sSNPs) in low-recombination regions of the genome. Using 5215 progeny from a genomic prediction experiment, we examined the fate of dSNPs over three breeding cycles. Adjusting for initial frequency, derived alleles at dSNPs reduced in frequency or were lost more often than other classes of SNPs. The highest-yielding lines in the experiment, as chosen by standard genomic prediction approaches, carried fewer homozygous dSNPs than randomly sampled lines from the same progeny cycle. In the final cycle of the experiment, progeny selected by genomic prediction had a mean of 5.6% fewer homozygous dSNPs relative to randomly chosen progeny from the same cycle.
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Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Emily E Vonderharr
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Justin C Fay
- Department of Biology, University of Rochester, New York 14627
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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