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Yin P, Fu X, Feng H, Yang Y, Xu J, Zhang X, Wang M, Ji S, Zhao B, Fang H, Du X, Li Y, Hu S, Li K, Xu S, Li Z, Liu F, Xiao Y, Wang Y, Li J, Yang X. Linkage and association mapping in multi-parental populations reveal the genetic basis of carotenoid variation in maize kernels. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2312-2326. [PMID: 38548388 PMCID: PMC11258976 DOI: 10.1111/pbi.14346] [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: 12/06/2023] [Revised: 03/02/2024] [Accepted: 03/14/2024] [Indexed: 07/21/2024]
Abstract
Carotenoids are indispensable to plants and critical components of the human diet. The carotenoid metabolic pathway is conserved across plant species, but our understanding of the genetic basis of carotenoid variation remains limited for the seeds of most cereal crops. To address this issue, we systematically performed linkage and association mapping for eight carotenoid traits using six recombinant inbred line (RIL) populations. Single linkage mapping (SLM) and joint linkage mapping (JLM) identified 77 unique additive QTLs and 104 pairs of epistatic QTLs. Among these QTLs, we identified 22 overlapping hotspots of additive and epistatic loci, highlighting the important contributions of some QTLs to carotenoid levels through additive or epistatic mechanisms. A genome-wide association study based on all RILs detected 244 candidate genes significantly associated with carotenoid traits, 23 of which were annotated as carotenoid pathway genes. Effect comparisons suggested that a small number of loci linked to pathway genes have substantial effects on carotenoid variation in our tested populations, but many loci not associated with pathway genes also make important contributions to carotenoid variation. We identified ZmPTOX as the causal gene for a QTL hotspot (Q10/JLM10/GWAS019); this gene encodes a putative plastid terminal oxidase that produces plastoquinone-9 used by two enzymes in the carotenoid pathway. Natural variants in the promoter and second exon of ZmPTOX were found to alter carotenoid levels. This comprehensive assessment of the genetic mechanisms underlying carotenoid variation establishes a foundation for rewiring carotenoid metabolism and accumulation for efficient carotenoid biofortification.
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Affiliation(s)
- Pengfei Yin
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Xiuyi Fu
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingMaize Research InstituteBeijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
| | - Haiying Feng
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Yanyan Yang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Jing Xu
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Xuan Zhang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Min Wang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Shenghui Ji
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Binghao Zhao
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Hui Fang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Xiaoxia Du
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Yaru Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Shuting Hu
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Kun Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Shutu Xu
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Zhigang Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
| | - Fang Liu
- Center for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
| | - Yingni Xiao
- Crops Research InstituteGuangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic ImprovementGuangzhouGuangdongChina
| | - Yuandong Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingMaize Research InstituteBeijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
| | - Jiansheng Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
- Center for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
| | - Xiaohong Yang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
- Center for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
- Frontiers Science Center for Molecular Design BreedingChina Agricultural UniversityBeijingChina
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2
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Lim I, Park YJ, Ha J. Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies. Sci Rep 2024; 14:5226. [PMID: 38433262 PMCID: PMC10909864 DOI: 10.1038/s41598-024-55581-w] [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: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024] Open
Abstract
The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice.
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Affiliation(s)
- Insu Lim
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
| | - Yong-Jin Park
- Department of Plant Sciences, Kongju National University, Yesan, 340-702, Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea.
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3
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Rennberger G, Branham SE, Wechter WP. Genome-Wide Association Study of Resistance to Pseudomonas syringae in the USDA Collection of Citrullus amarus. PLANT DISEASE 2023; 107:3464-3474. [PMID: 37129351 DOI: 10.1094/pdis-04-23-0795-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Pseudomonas leaf spot (PLS), caused by Pseudomonas syringae pv. syringae, is an emerging disease of watermelon in the United States with the potential to severely reduce yield under humid conditions. The genetic basis of resistance to this disease is not known and no resistant germplasm is available. Because Citrullus amarus is an important reservoir of resistance genes for the cultivated watermelon, C. lanatus, we screened the United States Department of Agriculture plant introduction collection of C. amarus for resistance to PLS. Accessions (n = 117) were phenotyped for their level of resistance to PLS in two separate tests. Accession means of percent leaf area affected ranged from 1.5 to 99.4%. The broad-sense heritability for the trait was 0.51. Whole-genome resequencing generated 2,126,759 single-nucleotide polymorphisms (SNPs) which were used to perform a genome-wide association study (GWAS) aimed at discovering molecular markers for resistance. Three different models-BLINK, FarmCPU, and MLM-were included in the GWAS analyses. BLINK and FarmCPU, which are multilocus models, found eight SNPs, located on chromosomes Ca01, Ca05, Ca06, Ca08, and Ca10, that were significantly associated with resistance to PLS. Two of these SNPs were found by both BLINK and FarmCPU. The MLM model did not detect any significant associations. BLINK and FarmCPU estimated an explained phenotypic variance of 43.6 and 28.5%, respectively, for SNP S6_19327000 and 25.0 and 26.0%, respectively, for SNP S1_33362258, the two most significant SNPs found. In total, 43 candidate genes with known involvement in disease resistance were discovered within the genomic intervals of seven of the eight peak SNPs. Eleven of the candidate genes that were found have been reported to be involved in resistance to P. syringae in other plant species. Two significant SNPs were within resistance genes previously documented to play important roles of plant resistance specific to P. syringae in other pathosystems. The SNPs identified in this study will be instrumental in finding causal genes involved in PLS resistance in watermelon and developing resistant germplasm through breeding.
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Affiliation(s)
- Gabriel Rennberger
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Vegetable Laboratory, Charleston, SC 29414
| | - Sandra E Branham
- Clemson University, Department of Plant and Environmental Sciences, Coastal Research and Education Center, Charleston, SC 29414
| | - William P Wechter
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Vegetable Laboratory, Charleston, SC 29414
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4
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Hawliczek A, Borzęcka E, Tofil K, Alachiotis N, Bolibok L, Gawroński P, Siekmann D, Hackauf B, Dušinský R, Švec M, Bolibok-Brągoszewska H. Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement. BMC PLANT BIOLOGY 2023; 23:323. [PMID: 37328739 PMCID: PMC10273710 DOI: 10.1186/s12870-023-04337-1] [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: 01/22/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection. RESULTS Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production. CONCLUSIONS Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.
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Affiliation(s)
- Anna Hawliczek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Nikolaos Alachiotis
- Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, Enschede, The Netherlands
| | - Leszek Bolibok
- Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | | | | | - Roman Dušinský
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Miroslav Švec
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland.
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5
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Sun G, Yu H, Wang P, Lopez-Guerrero M, Mural RV, Mizero ON, Grzybowski M, Song B, van Dijk K, Schachtman DP, Zhang C, Schnable JC. A role for heritable transcriptomic variation in maize adaptation to temperate environments. Genome Biol 2023; 24:55. [PMID: 36964601 PMCID: PMC10037803 DOI: 10.1186/s13059-023-02891-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/06/2023] [Indexed: 03/26/2023] Open
Abstract
Background Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. Result We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7614 genes. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in oxidation reduction, response to water deprivation, plastid biogenesis, protein biogenesis, and plant-pathogen interaction. Several genes involved in cell proliferation, flower development, DNA replication, and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments. Conclusion Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions. Supplementary information The online version contains supplementary material available at 10.1186/s13059-023-02891-3.
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Affiliation(s)
- Guangchao Sun
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Huihui Yu
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, USA
| | - Peng Wang
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Martha Lopez-Guerrero
- grid.24434.350000 0004 1937 0060Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Ravi V. Mural
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Olivier N. Mizero
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Marcin Grzybowski
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Baoxing Song
- grid.5386.8000000041936877XInstitute for Genomic Diversity, Cornell University, Ithaca, USA
| | - Karin van Dijk
- grid.24434.350000 0004 1937 0060Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Daniel P. Schachtman
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Chi Zhang
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, USA
| | - James C. Schnable
- grid.24434.350000 0004 1937 0060Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, USA
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
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6
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Andersson L, Purugganan M. Molecular genetic variation of animals and plants under domestication. Proc Natl Acad Sci U S A 2022; 119:e2122150119. [PMID: 35858409 PMCID: PMC9335317 DOI: 10.1073/pnas.2122150119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Domesticated plants and animals played crucial roles as models for evolutionary change by means of natural selection and for establishing the rules of inheritance, originally proposed by Charles Darwin and Gregor Mendel, respectively. Here, we review progress that has been made during the last 35 y in unraveling the molecular genetic variation underlying the stunning phenotypic diversity in crops and domesticated animals that inspired Mendel and Darwin. We notice that numerous domestication genes, crucial for the domestication process, have been identified in plants, whereas animal domestication appears to have a polygenic background with no obvious "domestication genes" involved. Although model organisms, such as Drosophila and Arabidopsis, have replaced domesticated species as models for basic research, the latter are still outstanding models for evolutionary research because phenotypic change in these species represents an evolutionary process over thousands of years. A consequence of this is that some alleles contributing to phenotypic diversity have evolved by accumulating multiple changes in the same gene. The continued molecular characterization of crops and farm animals with ever sharper tools is essential for future food security.
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Affiliation(s)
- Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
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7
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Selection-enriched genomic loci (SEGL) reveals genetic loci for environmental adaptation and photosynthetic productivity in Chlamydomonas reinhardtii. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Welsch R, Li L. Golden Rice—Lessons learned for inspiring future metabolic engineering strategies and synthetic biology solutions. Methods Enzymol 2022; 671:1-29. [DOI: 10.1016/bs.mie.2022.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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9
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Khoury CK, Brush S, Costich DE, Curry HA, de Haan S, Engels JMM, Guarino L, Hoban S, Mercer KL, Miller AJ, Nabhan GP, Perales HR, Richards C, Riggins C, Thormann I. Crop genetic erosion: understanding and responding to loss of crop diversity. THE NEW PHYTOLOGIST 2022; 233:84-118. [PMID: 34515358 DOI: 10.1111/nph.17733] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.
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Affiliation(s)
- Colin K Khoury
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537, Cali, Colombia
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- San Diego Botanic Garden, 230 Quail Gardens Dr., Encinitas, CA, 92024, USA
| | - Stephen Brush
- University of California Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, 56237, Texcoco, México
| | - Helen Anne Curry
- Department of History and Philosophy of Science, University of Cambridge, Free School Lane, Cambridge, CB2 3RH, UK
| | - Stef de Haan
- International Potato Center (CIP), Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru
| | | | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Sean Hoban
- The Morton Arboretum, The Center for Tree Science, 4100 IL-53, Lisle, IL, 60532, USA
| | - Kristin L Mercer
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Gary P Nabhan
- Southwest Center and Institute of the Environment, University of Arizona, 1401 E. First St., PO Box 210185, Tucson, AZ, 85721-0185, USA
| | - Hugo R Perales
- Departamento de Agroecología, El Colegio de la Frontera Sur, San Cristóbal, Chiapas, 29290, México
| | - Chris Richards
- National Laboratory for Genetic Resources Preservation, United States Department of Agriculture, Agricultural Research Service, 1111 South Mason Street, Fort Collins, CO, 80521, USA
| | - Chance Riggins
- Department of Crop Sciences, University of Illinois, 331 Edward R. Madigan Lab, 1201 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Imke Thormann
- Federal Office for Agriculture and Food (BLE), Information and Coordination Centre for Biological Diversity (IBV), Deichmanns Aue 29, 53179, Bonn, Germany
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10
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Kumar R, Sharma V, Suresh S, Ramrao DP, Veershetty A, Kumar S, Priscilla K, Hangargi B, Narasanna R, Pandey MK, Naik GR, Thomas S, Kumar A. Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples. Front Genet 2021; 12:637141. [PMID: 33889179 PMCID: PMC8055929 DOI: 10.3389/fgene.2021.637141] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.
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Affiliation(s)
- Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Srinivas Suresh
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Akash Veershetty
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Sharan Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Kagolla Priscilla
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Rahul Narasanna
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Manish Kumar Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Sherinmol Thomas
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University, Amarkantak, India
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11
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Ben Hdech D, Aubry C, Alibert B, Beucher D, Prosperi JM, Limami AM, Teulat B. Exploring natural diversity of Medicago truncatula reveals physiotypes and loci associated with the response of seedling performance to nitrate supply. PHYSIOLOGIA PLANTARUM 2020; 170:227-247. [PMID: 32492180 DOI: 10.1111/ppl.13144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/14/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Seedling pre-emergence is a critical phase of development for successful crop establishment because of its susceptibility to environmental conditions. In a context of reduced use of inorganic fertilizers, the genetic bases of the response of seedlings to nitrate supply received little attention. This issue is important even in legumes where nitrate absorption starts early after germination, before nodule development. Natural variation of traits characterizing seedling growth in the absence or presence of nitrate was investigated in a core collection of 192 accessions of Medicago truncatula. Plasticity indexes to the absence of nitrate were calculated. The genetic determinism of the traits was dissected by genome-wide association study (GWAS). The absence of nitrate affected seed biomass mobilization and root/shoot length ratio. However, the large range of genetic variability revealed different seedling performances within natural diversity. A principal component analysis (PCA) carried out with plasticity indexes highlighted four physiotypes of accessions differing in relationships between seedling elongation and seed biomass partitioning traits in response to the absence of nitrate. Finally, GWAS revealed 45 associations with single or combined traits corresponding to coordinates of accessions on PCA, as well as two clusters of genes encoding sugar transporters and glutathione transferases surrounding loci associated with seedling elongation traits.
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Affiliation(s)
- Douae Ben Hdech
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 42, rue Georges Morel, Beaucouzé, 49071, France
| | - Catherine Aubry
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 42, rue Georges Morel, Beaucouzé, 49071, France
| | - Bénédicte Alibert
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 42, rue Georges Morel, Beaucouzé, 49071, France
| | - Daniel Beucher
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 42, rue Georges Morel, Beaucouzé, 49071, France
| | - Jean-Marie Prosperi
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, 2, place P. Viala, Montpellier cedex 1, 34060, France
| | - Anis M Limami
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 42, rue Georges Morel, Beaucouzé, 49071, France
| | - Béatrice Teulat
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 42, rue Georges Morel, Beaucouzé, 49071, France
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12
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Wang M, Yang J, Wan J, Tao D, Zhou J, Yu D, Xu P. A hybrid sterile locus leads to the linkage drag of interspecific hybrid progenies. PLANT DIVERSITY 2020; 42:370-375. [PMID: 33134621 PMCID: PMC7584790 DOI: 10.1016/j.pld.2020.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 06/02/2023]
Abstract
Interspecific hybridization plays an important role in rice breeding by broadening access to desirable traits such as disease resistance and improving yields. However, interspecific hybridization is often hindered by hybrid sterility, linkage drag, and distorted segregation. To mine for favorable genes from Oryza glaberrima, we cultivated a series of BC4 introgression lines (ILs) of O. glaberrima in the japonica rice variety background (Dianjingyou 1) in which the IL-2769 (BC4F10) showed longer sterile lemmas, wider grains and spreading panicles compared with its receptor parent, suggesting that linkage drag may have occurred. Based on the BC5F2 population, a hybrid sterility locus, S20, a long sterile lemma locus, G1-g, and a new grain width quantitative trait locus (QTL), qGW7, were mapped in the linkage region about 15 centimorgan (cM) from the end of the short arm of chromosome 7. The hybrid sterility locus S20 from O. glaberrima eliminated male gametes of Oryza sativa, and male gametes carrying the alleles of O. sativa in the heterozygotes were aborted completely. In addition, the homozygotes presented a genotype of O. glaberrima, and homozygous O. sativa were not produced. Surprisingly, the linked traits G1-g and qGW7 showed similar segregation distortion. These results indicate that S20 was responsible for the linkage drag. As a large number of detected hybrid sterility loci are widely distributed on rice chromosomes, we suggest that hybrid sterility loci are the critical factors for the linkage drag in interspecific and subspecific hybridization of rice.
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Affiliation(s)
- Mianmian Wang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Yang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinpeng Wan
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, Yunnan, China
| | - Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, Yunnan, China
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Peng Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
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13
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Chettry U, Chrungoo NK. A multifocal approach towards understanding the complexities of carotenoid biosynthesis and accumulation in rice grains. Brief Funct Genomics 2020; 19:324-335. [PMID: 32240289 DOI: 10.1093/bfgp/elaa007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 11/12/2022] Open
Abstract
Carotenoids are mostly C40 terpenoids that participate in several important functions in plants including photosynthesis, responses to various forms of stress, signal transduction and photoprotection. While the antioxidant potential of carotenoids is of particular importance for human health, equally important is the role of β-carotene as the precursor for vitamin A in the human diet. Rice, which contributes upto 40% of dietary energy for mankind, contains very low level of β-carotene, thereby making it an important crop for enhancing β-carotene accumulation in its grains and consequently targeting vitamin A deficiency. Biosynthesis of carotenoids in the endosperm of white rice is blocked at the first enzymatic step wherein geranylgeranyl diphosphate is converted to phytoene by the action of phytoene synthase (PSY). Strategies aimed at enhancing β-carotene levels in the endosperm of white rice identified Narcissus pseudonarcissus (npPSY) and bacterial CRT1 as the regulators of the carotenoid biosynthetic pathway in rice. Besides transcriptional regulation of PSY, posttranscriptional regulation of PSY expression by OR gene, molecular synergism between ε-LCY and β-LCY and epigenetic control of CRITSO through SET DOMAIN containing protein appear to be the other regulatory nodes which regulate carotenoid biosynthesis and accumulation in rice grains. In this review, we elucidate a comprehensive and deeper understanding of the regulatory mechanisms of carotenoid metabolism in crops that will enable us to identify an effective tool to alleviate carotenoid content in rice grains.
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Affiliation(s)
- Upasna Chettry
- Department of Botany, North-Eastern Hill University, Shillong 793022, India
| | - Nikhil K Chrungoo
- Department of Botany, North-Eastern Hill University, Shillong 793022, India
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14
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Turner-Hissong SD, Mabry ME, Beissinger TM, Ross-Ibarra J, Pires JC. Evolutionary insights into plant breeding. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:93-100. [PMID: 32325397 DOI: 10.1016/j.pbi.2020.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/20/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Crop domestication is a fascinating area of study, as shown by a multitude of recent reviews. Coupled with the increasing availability of genomic and phenomic resources in numerous crop species, insights from evolutionary biology will enable a deeper understanding of the genetic architecture and short-term evolution of complex traits, which can be used to inform selection strategies. Future advances in crop improvement will rely on the integration of population genetics with plant breeding methodology, and the development of community resources to support research in a variety of crop life histories and reproductive strategies. We highlight recent advances related to the role of selective sweeps and demographic history in shaping genetic architecture, how these breakthroughs can inform selection strategies, and the application of precision gene editing to leverage these connections.
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Affiliation(s)
- Sarah D Turner-Hissong
- Center for Population Biology, University of California, Davis, CA, USA; Department of Evolution and Ecology, University of California, Davis, CA, USA.
| | - Makenzie E Mabry
- Bond Life Science Center and Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Timothy M Beissinger
- Division of Plant Breeding Methodology, Department of Crop Science, Georg-August-Universtät, Göttingen, Germany; Center for Integrated Breeding Research, Georg-August-Universtät, Göttingen, Germany
| | - Jeffrey Ross-Ibarra
- Center for Population Biology, University of California, Davis, CA, USA; Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - J Chris Pires
- Bond Life Science Center and Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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15
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Alves ML, Bento-Silva A, Carbas B, Gaspar D, Paulo M, Brites C, Mendes-Moreira P, Brites CM, Bronze MDR, Malosetti M, van Eeuwijk F, Vaz Patto MC. Alleles to Enhance Antioxidant Content in Maize-A Genome-Wide Association Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4051-4061. [PMID: 32141752 DOI: 10.1021/acs.jafc.9b07190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interest in antioxidant compound breeding in maize (Zea mays L.), a major food crop, has increased in recent years. However, breeding of antioxidant compounds in maize can be hampered, given the complex genetic nature of these compounds. In this work, we followed a genome-wide association approach, using a unique germplasm collection (containing Portuguese germplasm), to study the genetic basis of several antioxidants in maize. Sixty-seven genomic regions associated with seven antioxidant compounds and two color-related traits were identified. Several significant associations were located within or near genes involved in the carotenoid (Zm00001d036345) and tocopherol biosynthetic pathways (Zm00001d017746). Some indications of a negative selection against α-tocopherol levels were detected in the Portuguese maize germplasm. The strongest single nucleotide polymorphism (SNP)-trait associations and the SNP alleles with larger effect sizes were pinpointed and set as priority for future validation studies; these associations detected now constitute a benchmark for developing molecular selection tools for antioxidant compound selection in maize.
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Affiliation(s)
- Mara Lisa Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Andreia Bento-Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Bruna Carbas
- Instituto Nacional de Investigação Agrária e Veterinária, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Daniel Gaspar
- Instituto Politécnico de Coimbra, Escola Superior Agrária, Bencanta, 3045-601 Coimbra, Portugal
| | - Manuel Paulo
- Instituto Politécnico de Coimbra, Escola Superior Agrária, Bencanta, 3045-601 Coimbra, Portugal
| | - Cláudia Brites
- Instituto Politécnico de Coimbra, Escola Superior Agrária, Bencanta, 3045-601 Coimbra, Portugal
| | - Pedro Mendes-Moreira
- Instituto Politécnico de Coimbra, Escola Superior Agrária, Bencanta, 3045-601 Coimbra, Portugal
| | - Carla Moita Brites
- Instituto Nacional de Investigação Agrária e Veterinária, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Maria do Rosário Bronze
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Marcos Malosetti
- Biometris-Applied Statistics, Wageningen University, Radix, Building 107, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Fred van Eeuwijk
- Biometris-Applied Statistics, Wageningen University, Radix, Building 107, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
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16
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Genome-wide association analysis of stripe rust resistance loci in wheat accessions from southwestern China. J Appl Genet 2020; 61:37-50. [PMID: 31912452 PMCID: PMC6969011 DOI: 10.1007/s13353-019-00533-8] [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: 05/04/2019] [Revised: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 11/17/2022]
Abstract
Wheat stripe rust can cause considerable yield losses, and genetic resistance is the most effective approach for controlling the disease. To identify the genomic regions responsible for Puccinia striiformis f. sp. tritici (Pst) resistance in a set of winter wheat strains mainly from southwestern China, and to identify DNA markers in these regions, we carried out a genome-wide association study (GWAS) of 120 China winter wheat accessions using single nucleotide polymorphism (SNP) markers from 90K wheat SNP arrays. In total, 16 SNP loci were significantly associated with wheat stripe rust in field and greenhouse trials. Of these, three distinctive SNPs on chromosomes 1B, 4A, and 6A were identified at a site in Mianyang in 2014, where the most prevalent wheat stripe rust races since 2009 have been V26 (G22-9, G22-14). This suggests that the three SNP loci were linked to the new quantitative trait loci (QTL)/genes resistant to the V26 races. Germplasm with immunity to Pst is a good source of stripe rust resistance for breeding, and after further validation, SNPs closely linked to resistance QTLs/genes could be converted into user-friendly markers and facilitate marker-assisted selection to improve wheat stripe rust resistance.
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17
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Li J, Chen GB, Rasheed A, Li D, Sonder K, Zavala Espinosa C, Wang J, Costich DE, Schnable PS, Hearne SJ, Li H. Identifying loci with breeding potential across temperate and tropical adaptation via EigenGWAS and EnvGWAS. Mol Ecol 2019; 28:3544-3560. [PMID: 31287919 PMCID: PMC6851670 DOI: 10.1111/mec.15169] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 06/20/2019] [Indexed: 02/01/2023]
Abstract
Understanding the genomic basis of adaptation in maize is important for gene discovery and the improvement of breeding germplasm, but much remains a mystery in spite of significant population genetics and archaeological research. Identifying the signals underpinning adaptation are challenging as adaptation often coincided with genetic drift, and the base genomic diversity of the species in massive. In this study, tGBS technology was used to genotype 1,143 diverse maize accessions including landraces collected from 20 countries and elite breeding lines of tropical lowland, highland, subtropical/midaltitude and temperate ecological zones. Based on 355,442 high‐quality single nucleotide polymorphisms, 13 genomic regions were detected as being under selection using the bottom‐up searching strategy, EigenGWAS. Of the 13 selection regions, 10 were first reported, two were associated with environmental parameters via EnvGWAS, and 146 genes were enriched. Combining large‐scale genomic and ecological data in this diverse maize panel, our study supports a polygenic adaptation model of maize and offers a framework to enhance our understanding of both the mechanistic basis and the evolutionary consequences of maize domestication and adaptation. The regions identified here are promising candidates for further, targeted exploration to identify beneficial alleles and haplotypes for deployment in maize breeding.
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Affiliation(s)
- Jing Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guo-Bo Chen
- Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Delin Li
- Data Biotech (Beijing) Co., Ltd, Beijing, China.,College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Kai Sonder
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Jiankang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Patrick S Schnable
- Data Biotech (Beijing) Co., Ltd, Beijing, China.,College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.,Data2Bio LLC, Ames, IA, USA.,Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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18
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Mapping loci controlling fatty acid profiles, oil and protein content by genome-wide association study in Brassica napus. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2018.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Wurtzel ET. Changing Form and Function through Carotenoids and Synthetic Biology. PLANT PHYSIOLOGY 2019; 179:830-843. [PMID: 30361256 PMCID: PMC6393808 DOI: 10.1104/pp.18.01122] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/06/2018] [Indexed: 05/06/2023]
Abstract
The diverse structures and multifaceted roles of carotenoids make these colorful pigments attractive targets for synthetic biology.
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Affiliation(s)
- Eleanore T Wurtzel
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York 10468
- The Graduate School and University Center-CUNY, New York, New York 10016-4309
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20
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Cultrera NGM, Sarri V, Lucentini L, Ceccarelli M, Alagna F, Mariotti R, Mousavi S, Ruiz CG, Baldoni L. High Levels of Variation Within Gene Sequences of Olea europaea L. FRONTIERS IN PLANT SCIENCE 2019; 9:1932. [PMID: 30671076 PMCID: PMC6331486 DOI: 10.3389/fpls.2018.01932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/12/2018] [Indexed: 05/08/2023]
Abstract
Gene sequence variation in cultivated olive (Olea europaea L. subsp. europaea var. europaea), the most important oil tree crop of the Mediterranean basin, has been poorly evaluated up to now. A deep sequence analysis of fragments of four genes, OeACP1, OeACP2, OeLUS and OeSUT1, in 90 cultivars, revealed a wide range of polymorphisms along all recognized allele forms and unexpected allele frequencies and genotype combinations. High linkage values among most polymorphisms were recorded within each gene fragment. The great sequence variability corresponded to a low number of alleles and, surprisingly, to a small fraction of genotype combinations. The distribution, frequency, and combination of the different alleles at each locus is possibly due to natural and human pressures, such as selection, ancestrality, or fitness. Phylogenetic analyses of allele sequences showed distant and complex patterns of relationships among cultivated olives, intermixed with other related forms, highlighting an evolutionary connection between olive cultivars and the O. europaea subspecies cuspidata and cerasiformis. This study demonstrates how a detailed and complete sequence analysis of a few gene portions and a thorough genotyping on a representative set of cultivars can clarify important issues related to sequence polymorphisms, reconstructing the phylogeny of alleles, as well as the genotype combinations. The identification of regions representing blocks of recombination could reveal polymorphisms that represent putatively functional markers. Indeed, specific mutations found on the analyzed OeACP1 and OeACP2 fragments seem to be correlated to the fruit weight.
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Affiliation(s)
- Nicolò G. M. Cultrera
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Vania Sarri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Livia Lucentini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Fiammetta Alagna
- ENEA Italian National Agency for New Technologies Energy and Sustainable Economic Development, Trisaia Research Center, Rotondella, Italy
| | - Roberto Mariotti
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Soraya Mousavi
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | | | - Luciana Baldoni
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
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21
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Molecular analysis of mutant granule-bound starch synthase-I ( waxy1) gene in diverse waxy maize inbreds. 3 Biotech 2019; 9:3. [PMID: 30555769 DOI: 10.1007/s13205-018-1530-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Waxy corn is popular beacuse of its high amylopectin due to mutation in granule-bound starch synthase-I or Waxy1 (Wx1) gene. Here, we characterized the wx1 allele among 24 diverse waxy inbreds using gene-based markers. A total of 29 alleles with average of 1.81 alleles/locus were observed. Major allele frequency varied from 0.42 to 1.00, with mean of 0.74. The polymorphism information content ranged from 0.00 to 0.56 (average 0.24). Three simple sequence repeat markers, viz., phi027, phi022 and phi061 were more polymorphic in the study. The mean heterozygosity was 0.04, which indicated attainment of higher levels of homozygosity. Dissimilarity coefficient varied from 0.00 to 0.90 with average of 0.51. Seventeen diverse haplotypes of wx1 allele were observed that was consistent with the pedigree. Cluster analyses grouped 24 genotypes into two main clusters each having sub-clusters. The information generated here possesses great potential for improvement of high amylopectin in maize through marker-assisted selection. This is the first report of molecular dissection of wx1 gene among the novel waxy inbreds developed in India.
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22
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Zhu G, Wang S, Huang Z, Zhang S, Liao Q, Zhang C, Lin T, Qin M, Peng M, Yang C, Cao X, Han X, Wang X, van der Knaap E, Zhang Z, Cui X, Klee H, Fernie AR, Luo J, Huang S. Rewiring of the Fruit Metabolome in Tomato Breeding. Cell 2018; 172:249-261.e12. [PMID: 29328914 DOI: 10.1016/j.cell.2017.12.019] [Citation(s) in RCA: 470] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/03/2017] [Accepted: 12/15/2017] [Indexed: 11/29/2022]
Abstract
Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes. Selection of five major loci reduced the accumulation of anti-nutritional steroidal glycoalkaloids in ripened fruits, rendering the fruit more edible. Breeding for pink tomatoes modified the content of over 100 metabolites. The introgression of resistance genes from wild relatives in cultivars also resulted in major and unexpected metabolic changes. The study reveals a multi-omics view of the metabolic breeding history of tomato, as well as provides insights into metabolome-assisted breeding and plant biology.
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Affiliation(s)
- Guangtao Zhu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zejun Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuaibin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qinggang Liao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Chunzhi Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Tao Lin
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Mao Qin
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Meng Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xue Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Han
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Xiaoxuan Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Harry Klee
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL 32611, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 144776, Germany; Center of Plant System Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Tropical Agriculture and Forestry of Hainan University, Haikou, Hainan 572208, China.
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Parins-Fukuchi C. Use of Continuous Traits Can Improve Morphological Phylogenetics. Syst Biol 2018; 67:328-339. [PMID: 28945906 DOI: 10.1093/sysbio/syx072] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 08/30/2017] [Indexed: 12/21/2022] Open
Abstract
The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modeling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modeling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character coding of discrete characters. The often subjective nature of discrete character coding can generate discordant results that are rooted in individual researchers' subjective interpretations. Employing continuous measurements to infer phylogenies may alleviate some of these issues. Although not widely used in the inference of topology, models describing the evolution of continuous characters have been well examined, and their statistical behavior is well understood. Also, continuous measurements avoid the substantial ambiguity often associated with the assignment of discrete characters to states. I present a set of simulations to determine whether use of continuous characters is a feasible alternative or supplement to discrete characters for inferring phylogeny. I compare relative reconstruction accuracy by inferring phylogenies from simulated continuous and discrete characters. These tests demonstrate significant promise for continuous traits by demonstrating their higher overall accuracy as compared to reconstruction from discrete characters under Mk when simulated under unbounded Brownian motion, and equal performance when simulated under an Ornstein-Uhlenbeck model. Continuous characters also perform reasonably well in the presence of covariance between sites. I argue that inferring phylogenies directly from continuous traits may be benefit efforts to maximize phylogenetic information in morphological data sets by preserving larger variation in state space compared to many discretization schemes. I also suggest that the use of continuous trait models in phylogenetic reconstruction may alleviate potential concerns of discrete character model adequacy, while identifying areas that require further study in this area. This study provides an initial controlled demonstration of the efficacy of continuous characters in phylogenetic inference.
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Affiliation(s)
- Caroline Parins-Fukuchi
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA
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24
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Wang Z, Wang L, Wang Z, Lu BR. Non-random transmission of parental alleles into crop-wild and crop-weed hybrid lineages separated by a transgene and neutral identifiers in rice. Sci Rep 2017; 7:10436. [PMID: 28874702 PMCID: PMC5585250 DOI: 10.1038/s41598-017-10596-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/10/2017] [Indexed: 11/09/2022] Open
Abstract
It is essential to assess environmental impact of transgene flow from genetically engineered crops to their wild or weedy relatives before commercialization. Measuring comparative trials of fitness in the transgene-flow-resulted hybrids plays the key role in the assessment, where the segregated isogenic hybrid lineages/subpopulations with or without a transgene of the same genomic background are involved. Here, we report substantial genomic differentiation between transgene-present and -absent lineages (F2-F3) divided by a glyphosate-resistance transgene from a crop-wild/weed hybrid population in rice. We further confirmed that such differentiation is attributed to increased frequencies of crop-parent alleles in transgenic hybrid lineages at multiple loci across the genome, as estimated by SSR (simple sequence repeat) markers. Such preferential transmission of parental alleles was also found in equally divided crop-wild/weed hybrid lineages with or without a particular neutral SSR identifier. We conclude that selecting either a transgene or neutral marker as an identifier to create hybrid lineages will result in different genomic background of the lineages due to non-random transmission of parental alleles. Non-random allele transmission may misrepresent the outcomes of fitness effects. We therefore propose seeking other means to evaluate fitness effects of transgenes for assessing environmental impact caused by crop-to-wild/weed gene flow.
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Affiliation(s)
- Zhe Wang
- Ministry of Education Key Laboratory for biodiversity science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai, 200433, China
| | - Lei Wang
- Ministry of Education Key Laboratory for biodiversity science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai, 200433, China
| | - Zhi Wang
- Ministry of Education Key Laboratory for biodiversity science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai, 200433, China
| | - Bao-Rong Lu
- Ministry of Education Key Laboratory for biodiversity science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai, 200433, China.
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25
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Zhong L, Yang Q, Yan X, Yu C, Su L, Zhang X, Zhu Y. Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soya bean [Glycine max (L.) Merr.]. Mol Ecol 2017; 26:4686-4699. [PMID: 28627128 DOI: 10.1111/mec.14209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 05/24/2017] [Accepted: 06/06/2017] [Indexed: 02/02/2023]
Abstract
Determinate growth habit is an agronomically important trait associated with domestication in soya bean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four nonsynonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb, were identified, which constitute the soft sweeps for the adaptation. These variable-sized sweeps substantially reflected the strength and timing of selection and indicated that the selection on the alleles had been completed rapidly within half a century. Statistics of EHH, iHS, H12 and H2/H1 based on haplotype data had the power to detect the soft sweeps, revealing distinct signatures of extensive long-range LD and haplotype homozygosity, and multiple frequent adaptive haplotypes. A haplotype network constructed for Dt1 and a phylogenetic tree based on its extended haplotype block implied independent sources of the adaptive alleles through de novo mutations or rare standing variation in quick succession during the selective phase, strongly supporting multiple origins of the determinacy. We propose that the adaptation of soya bean determinacy is guided by a model of soft sweeps and that this model might be indispensable during crop domestication or evolution.
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Affiliation(s)
- Limei Zhong
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Qiaomei Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Chao Yu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Liu Su
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Xifeng Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
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26
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Swarts K, Gutaker RM, Benz B, Blake M, Bukowski R, Holland J, Kruse-Peeples M, Lepak N, Prim L, Romay MC, Ross-Ibarra J, Sanchez-Gonzalez JDJ, Schmidt C, Schuenemann VJ, Krause J, Matson RG, Weigel D, Buckler ES, Burbano HA. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 2017; 357:512-515. [DOI: 10.1126/science.aam9425] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/29/2017] [Indexed: 01/24/2023]
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27
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Genome-wide indel/SSR scanning reveals significant loci associated with excellent agronomic traits of a cabbage (Brassica oleracea) elite parental line '01-20'. Sci Rep 2017; 7:41696. [PMID: 28164997 PMCID: PMC5292705 DOI: 10.1038/srep41696] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/23/2016] [Indexed: 01/05/2023] Open
Abstract
Elite parental lines are of great significance to crop breeding. To discover unique genomic loci associated with excellent economic traits in the elite cabbage inbred-line ‘01–20’, we performed comparisons of phenotypes as well as whole-genome insertion-deletion/simple sequence repeat loci between ‘01–20’ and each of its five sister lines. ‘01–20’ has a range of excellent agronomic traits, including early-maturing, and improvements in plant type and leaf colour. Eight unique loci were discovered for ‘01–20’ and ‘01-07-258’, another elite line similar to ‘01–20’ at the whole-genome level. In addition, two excellent double-haploid lines derived from a cross of ‘01–20’ also inherited these loci. Based on the quantitative trait locus association results, five of these loci were found to be associated with important agronomic traits, which could explain why the elite parent ‘01–20’ possesses greener outer leaves, a more compact and upright plant-type, rounder head, shorter core length, and better taste. Additionally, some of these loci have clustering effects for quantitative trait loci associated with different traits; therefore, important genes in these regions were analysed. The obtained results should enable marker-assisted multi-trait selection at the whole-genome level in cabbage breeding and provide insights into significant genome loci and their breeding effects.
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28
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Structure and Origin of the White Cap Locus and Its Role in Evolution of Grain Color in Maize. Genetics 2017; 206:135-150. [PMID: 28159756 PMCID: PMC5419465 DOI: 10.1534/genetics.116.198911] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/22/2017] [Indexed: 11/18/2022] Open
Abstract
Selection for yellow- and white-grain types has been central to postdomestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the Yellow1 (Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factor White Cap (Wc). We show that the Wc locus contains multiple, tandem copies of a Carotenoid cleavage dioxygenase 1 (Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 22 teosinte accessions, reveals that Wc is exclusive to maize, where it is prevalent in white-grain (y1) varieties. Moreover, Ccd1 copy number varies extensively among Wc alleles (from 1 to 23 copies), and confers a proportional range of Ccd1 expression in diverse organs. We propose that this dynamic source of quantitative variation in Ccd1 expression was created in maize shortly after domestication by a two-step, Tam3L transposon-mediated process. First, a chromosome segment containing Ccd1 and several nearby genes duplicated at a position 1.9 Mb proximal to the progenitor Ccd1r locus on chromosome 9. Second, a subsequent interaction of Tam3L transposons at the new locus created a 28-kb tandem duplication, setting up expansion of Ccd1 copy number by unequal crossing over. In this way, transposon-mediated variation in copy number at the Wc locus generated phenotypic variation that provided a foundation for breeding and selection of white-grain color in maize.
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29
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Jittham O, Fu X, Xu J, Chander S, Li J, Yang X. Genetic dissection of carotenoids in maize kernels using high-density single nucleotide polymorphism markers in a recombinant inbred line population. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2016.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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30
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Zhang H, Mittal N, Leamy LJ, Barazani O, Song B. Back into the wild-Apply untapped genetic diversity of wild relatives for crop improvement. Evol Appl 2017; 10:5-24. [PMID: 28035232 PMCID: PMC5192947 DOI: 10.1111/eva.12434] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/07/2016] [Indexed: 12/18/2022] Open
Abstract
Deleterious effects of climate change and human activities, as well as diverse environmental stresses, present critical challenges to food production and the maintenance of natural diversity. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enables them to thrive in marginal lands. However, considering the diverse interactions between crops and environmental factors, it is surprising that evolutionary principles have been underexploited in addressing these food and environmental challenges. Compared with domesticated cultivars, crop wild relatives (CWRs) have been challenged in natural environments for thousands of years and maintain a much higher level of genetic diversity. In this review, we highlight the significance of CWRs for crop improvement by providing examples of CWRs that have been used to increase biotic and abiotic stress resistance/tolerance and overall yield in various crop species. We also discuss the surge of advanced biotechnologies, such as next-generation sequencing technologies and omics, with particular emphasis on how they have facilitated gene discovery in CWRs. We end the review by discussing the available resources and conservation of CWRs, including the urgent need for CWR prioritization and collection to ensure continuous crop improvement for food sustainability.
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Affiliation(s)
- Hengyou Zhang
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Neha Mittal
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Larry J. Leamy
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Oz Barazani
- The Institute for Plant SciencesIsrael Plant Gene BankAgricultural Research OrganizationBet DaganIsrael
| | - Bao‐Hua Song
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
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31
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Gao Y, Liu Z, Faris JD, Richards J, Brueggeman RS, Li X, Oliver RP, McDonald BA, Friesen TL. Validation of Genome-Wide Association Studies as a Tool to Identify Virulence Factors in Parastagonospora nodorum. PHYTOPATHOLOGY 2016; 106:1177-1185. [PMID: 27442533 DOI: 10.1094/phyto-02-16-0113-fi] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Parastagonospora nodorum is a necrotrophic fungal pathogen causing Septoria nodorum blotch on wheat. We have identified nine necrotrophic effector-host dominant sensitivity gene interactions, and we have cloned three of the necrotrophic effector genes, including SnToxA, SnTox1, and SnTox3. Because sexual populations of P. nodorum are difficult to develop under lab conditions, genome-wide association study (GWAS) is the best population genomic approach to identify genomic regions associated with traits using natural populations. In this article, we used a global collection of 191 P. nodorum isolates from which we identified 2,983 single-nucleotide polymorphism (SNP) markers and gene markers for SnToxA and SnTox3 to evaluate the power of GWAS on two popular wheat breeding lines that were sensitive to SnToxA and SnTox3. Strong marker trait associations (MTA) with P. nodorum virulence that mapped to SnTox3 and SnToxA were first identified using the marker set described above. A novel locus in the P. nodorum genome associated with virulence was also identified as a result of this analysis. To evaluate whether a sufficient level of marker saturation was available, we designed a set of primers every 1 kb in the genomic regions containing SnToxA and SnTox3. Polymerase chain reaction amplification was performed across the 191 isolates and the presence/absence polymorphism was scored and used as the genotype. The marker proximity necessary to identify MTA flanking SnToxA and SnTox3 ranged from 4 to 5 and 1 to 7 kb, respectively. Similar analysis was performed on the novel locus. Using a 45% missing data threshold, two more SNP were identified spanning a 4.6-kb genomic region at the novel locus. These results showed that the rate of linkage disequilibrium (LD) decay in P. nodorum and, likely, other fungi is high compared with plants and animals. The fast LD decay in P. nodorum is an advantage only if sufficient marker density is attained. Based on our results with the SnToxA and SnTox3 regions, markers are needed every 9 or 8 kb, respectively, or in every gene, to guarantee that genes associated with a quantitative trait such as virulence are not missed.
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Affiliation(s)
- Yuanyuan Gao
- First, second, fourth, fifth, and ninth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; third and ninth authors: United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Fargo, ND, 58102; sixth author: Department of Plant Science, North Dakota State University, Fargo; seventh author: Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA 6102, Australia; and eighth author: Institute of Integrative Biology, Plant Pathology Group, Swiss Federal Institute of Technology, ETH Zentrum, LFW, CH-8092 Zürich, Switzerland
| | - Zhaohui Liu
- First, second, fourth, fifth, and ninth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; third and ninth authors: United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Fargo, ND, 58102; sixth author: Department of Plant Science, North Dakota State University, Fargo; seventh author: Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA 6102, Australia; and eighth author: Institute of Integrative Biology, Plant Pathology Group, Swiss Federal Institute of Technology, ETH Zentrum, LFW, CH-8092 Zürich, Switzerland
| | - Justin D Faris
- First, second, fourth, fifth, and ninth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; third and ninth authors: United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Fargo, ND, 58102; sixth author: Department of Plant Science, North Dakota State University, Fargo; seventh author: Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA 6102, Australia; and eighth author: Institute of Integrative Biology, Plant Pathology Group, Swiss Federal Institute of Technology, ETH Zentrum, LFW, CH-8092 Zürich, Switzerland
| | - Jonathan Richards
- First, second, fourth, fifth, and ninth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; third and ninth authors: United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Fargo, ND, 58102; sixth author: Department of Plant Science, North Dakota State University, Fargo; seventh author: Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA 6102, Australia; and eighth author: Institute of Integrative Biology, Plant Pathology Group, Swiss Federal Institute of Technology, ETH Zentrum, LFW, CH-8092 Zürich, Switzerland
| | - Robert S Brueggeman
- First, second, fourth, fifth, and ninth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; third and ninth authors: United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Fargo, ND, 58102; sixth author: Department of Plant Science, North Dakota State University, Fargo; seventh author: Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA 6102, Australia; and eighth author: Institute of Integrative Biology, Plant Pathology Group, Swiss Federal Institute of Technology, ETH Zentrum, LFW, CH-8092 Zürich, Switzerland
| | - Xuehui Li
- First, second, fourth, fifth, and ninth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; third and ninth authors: United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Fargo, ND, 58102; sixth author: Department of Plant Science, North Dakota State University, Fargo; seventh author: Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA 6102, Australia; and eighth author: Institute of Integrative Biology, Plant Pathology Group, Swiss Federal Institute of Technology, ETH Zentrum, LFW, CH-8092 Zürich, Switzerland
| | - Richard P Oliver
- First, second, fourth, fifth, and ninth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; third and ninth authors: United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Fargo, ND, 58102; sixth author: Department of Plant Science, North Dakota State University, Fargo; seventh author: Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA 6102, Australia; and eighth author: Institute of Integrative Biology, Plant Pathology Group, Swiss Federal Institute of Technology, ETH Zentrum, LFW, CH-8092 Zürich, Switzerland
| | - Bruce A McDonald
- First, second, fourth, fifth, and ninth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; third and ninth authors: United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Fargo, ND, 58102; sixth author: Department of Plant Science, North Dakota State University, Fargo; seventh author: Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA 6102, Australia; and eighth author: Institute of Integrative Biology, Plant Pathology Group, Swiss Federal Institute of Technology, ETH Zentrum, LFW, CH-8092 Zürich, Switzerland
| | - Timothy L Friesen
- First, second, fourth, fifth, and ninth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; third and ninth authors: United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Fargo, ND, 58102; sixth author: Department of Plant Science, North Dakota State University, Fargo; seventh author: Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA 6102, Australia; and eighth author: Institute of Integrative Biology, Plant Pathology Group, Swiss Federal Institute of Technology, ETH Zentrum, LFW, CH-8092 Zürich, Switzerland
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32
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Muto C, Ishikawa R, Olsen KM, Kawano K, Bounphanousay C, Matoh T, Sato YI. Genetic diversity of the wx flanking region in rice landraces in northern Laos. BREEDING SCIENCE 2016; 66:580-590. [PMID: 27795683 PMCID: PMC5010311 DOI: 10.1270/jsbbs.16032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/11/2016] [Indexed: 05/07/2023]
Abstract
A glutinous texture of endosperm is one of the important traits of rice (Oyza sativa L.). Northern Laos is known as a center of glutinous rice diversity. We genotyped INDEL, SSR and SNP markers in a sample of 297 rice landraces collected in northern Laos. These glutinous varieties were confirmed to share a loss-of-function mutation in Granule bound starch synthase I (Wx). INDEL markers revealed a high frequency of recombinant genotypes between indica and japonica. Principal component analysis using SSR genotypes of Wx flanking region revealed that glutinous indica landraces were scattered between non-glutinous indica and glutinous-japonica types. High ratios of heterozygosity were found especially in glutinous indica. Haplotype analysis using SNP markers around Wx locus revealed that glutinous indica landraces would have a few chromosome segments of glutinous japonica. Frequent recombinations were confirmed outside of this region in glutinous indica. This intricate genetic structure of landraces suggested that glutinous indica landraces in Laos were generated through repeated natural crossing with glutinous-japonica landraces and severe selection by local farmers.
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Affiliation(s)
- Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Research Organization,
Tsukuba, Ibaraki 305-8602,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8560,
Japan
- Corresponding author (e-mail: )
| | - Kenneth M. Olsen
- Biology Department, Washington University,
St. Louis 63130-4899,
USA
| | - Kazuaki Kawano
- Institute of Southern Cultural Folklore,
Kirishima, Kagoshima 899-4201,
Japan
| | - Chay Bounphanousay
- Agricultural Research Centre, National Agriculture and Forestry Research Institute,
Nongviengkham, Vientiane 7170,
Lao P.D.R
| | - Toru Matoh
- Graduate School of Agriculture, Kyoto University,
Kyoto 606-8502,
Japan
| | - Yo-Ichiro Sato
- National Institutes for the Humanities,
Minato-ku, Tokyo 105-0001,
Japan
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33
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Xu J, Li Z, Yang H, Yang X, Chen C, Li H. Genetic Diversity and Molecular Evolution of a Violaxanthin De-epoxidase Gene in Maize. Front Genet 2016; 7:131. [PMID: 27507987 PMCID: PMC4960258 DOI: 10.3389/fgene.2016.00131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 07/07/2016] [Indexed: 12/30/2022] Open
Abstract
Violaxanthin de-epoxidase (VDE) has a critical role in the carotenoid biosynthesis pathway, which is involved in protecting the photosynthesis apparatus from damage caused by excessive light. Here, a VDE gene in maize, ZmVDE1, was cloned and shown to have functional domains in common with the gramineous VDE protein. Candidate gene association analysis indicated that no polymorphic sites in ZmVDE1 were significant association with any of the examined carotenoid-related traits at P = 0.05 in an association panel containing 155 maize inbred lines. Nucleotide diversity analysis of VDE1 in maize and teosinte indicated that its exon had less genetic variation, consistent with the conserved function of VDE1 in plants. In addition, dramatically reduced nucleotide diversity, fewer haplotypes and a significantly negative parameter deviation for Tajima’s D test of ZmVDE1 in maize and teosinte suggested that a potential selective force had acted across the ZmVDE1 locus. We further identified a 4.2 Mb selective sweep with low recombination surrounding the ZmVDE1 locus that resulted in severely reduced nucleotide diversity on chromosome 2. Collectively, natural selection and the conserved domains of ZmVDE1 might show an important role in the xanthophyll cycle of the carotenoid biosynthesis pathway.
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Affiliation(s)
- Jing Xu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural UniversityTai'an, China; Key Laboratory of Crop Genomics and Genetic Improvement, National Maize Improvement Center of China, China Agricultural UniversityBeijing, China
| | - Zhigang Li
- Key Laboratory of Crop Genomics and Genetic Improvement, National Maize Improvement Center of China, China Agricultural University Beijing, China
| | - Haorui Yang
- Key Laboratory of Crop Genomics and Genetic Improvement, National Maize Improvement Center of China, China Agricultural University Beijing, China
| | - Xiaohong Yang
- Key Laboratory of Crop Genomics and Genetic Improvement, National Maize Improvement Center of China, China Agricultural University Beijing, China
| | - Cuixia Chen
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University Tai'an, China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan Jinan, China
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Esvelt Klos K, Huang YF, Bekele WA, Obert DE, Babiker E, Beattie AD, Bjørnstad Å, Bonman JM, Carson ML, Chao S, Gnanesh BN, Griffiths I, Harrison SA, Howarth CJ, Hu G, Ibrahim A, Islamovic E, Jackson EW, Jannink JL, Kolb FL, McMullen MS, Mitchell Fetch J, Murphy JP, Ohm HW, Rines HW, Rossnagel BG, Schlueter JA, Sorrells ME, Wight CP, Yan W, Tinker NA. Population Genomics Related to Adaptation in Elite Oat Germplasm. THE PLANT GENOME 2016; 9. [PMID: 27898836 DOI: 10.3835/plantgenome2015.10.0103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype-phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24.
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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet 2016; 48:657-66. [PMID: 27158781 DOI: 10.1038/ng.3565] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 04/11/2016] [Indexed: 11/09/2022]
Abstract
We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.
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Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster. Genetics 2016; 203:863-80. [PMID: 27098909 DOI: 10.1534/genetics.115.184002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 03/25/2016] [Indexed: 12/20/2022] Open
Abstract
The extent to which selection and demography impact patterns of genetic diversity in natural populations of Drosophila melanogaster is yet to be fully understood. We previously observed that linkage disequilibrium (LD) at scales of ∼10 kb in the Drosophila Genetic Reference Panel (DGRP), consisting of 145 inbred strains from Raleigh, North Carolina, measured both between pairs of sites and as haplotype homozygosity, is elevated above neutral demographic expectations. We also demonstrated that signatures of strong and recent soft sweeps are abundant. However, the extent to which these patterns are specific to this derived and admixed population is unknown. It is also unclear whether these patterns are a consequence of the extensive inbreeding performed to generate the DGRP data. Here we analyze LD statistics in a sample of >100 fully-sequenced strains from Zambia; an ancestral population to the Raleigh population that has experienced little to no admixture and was generated by sequencing haploid embryos rather than inbred strains. We find an elevation in long-range LD and haplotype homozygosity compared to neutral expectations in the Zambian sample, thus showing the elevation in LD is not specific to the DGRP data set. This elevation in LD and haplotype structure remains even after controlling for possible confounders including genomic inversions, admixture, population substructure, close relatedness of individual strains, and recombination rate variation. Furthermore, signatures of partial soft sweeps similar to those found in the DGRP as well as partial hard sweeps are common in Zambia. These results suggest that while the selective forces and sources of adaptive mutations may differ in Zambia and Raleigh, elevated long-range LD and signatures of soft sweeps are generic in D. melanogaster.
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Akagi T, Hanada T, Yaegaki H, Gradziel TM, Tao R. Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication. DNA Res 2016; 23:271-82. [PMID: 27085183 PMCID: PMC4909313 DOI: 10.1093/dnares/dsw014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/02/2016] [Indexed: 01/19/2023] Open
Abstract
Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.
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Affiliation(s)
- Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan
| | - Toshio Hanada
- Apple Research Division, NARO Institute of Fruit Tree Science, Morioka 020-0123, Japan
| | - Hideaki Yaegaki
- Breeding and Pest Management Division, NARO Institute, Tsukuba, Ibaragi 305-8605, Japan
| | - Thomas M Gradziel
- Department of Plant Sciences, University of California Davis, CA 95616, USA
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan
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Pérez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. PLANT MOLECULAR BIOLOGY 2016; 90:635-44. [PMID: 26085172 PMCID: PMC4819786 DOI: 10.1007/s11103-015-0337-7] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/04/2015] [Indexed: 05/18/2023]
Abstract
The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.
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Affiliation(s)
- Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000, Brazil
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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Rezaei MK, Deokar A, Tar'an B. Identification and Expression Analysis of Candidate Genes Involved in Carotenoid Biosynthesis in Chickpea Seeds. FRONTIERS IN PLANT SCIENCE 2016; 7:1867. [PMID: 28018400 PMCID: PMC5157839 DOI: 10.3389/fpls.2016.01867] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/25/2016] [Indexed: 05/03/2023]
Abstract
Plant carotenoids have a key role in preventing various diseases in human because of their antioxidant and provitamin A properties. Chickpea is a good source of carotenoid among legumes and its diverse germplasm and genome accessibility makes it a good model for carotenogenesis studies. The structure, location, and copy numbers of genes involved in carotenoid biosynthesis were retrieved from the chickpea genome. The majority of the single nucleotide polymorphism (SNPs) within these genes across five diverse chickpea cultivars was synonymous mutation. We examined the expression of the carotenogenesis genes and their association with carotenoid concentration at different seed development stages of five chickpea cultivars. Total carotenoid concentration ranged from 22 μg g-1 in yellow cotyledon kabuli to 44 μg g-1 in green cotyledon desi at 32 days post anthesis (DPA). The majority of carotenoids in chickpea seeds consists of lutein and zeaxanthin. The expression of the selected 19 genes involved in carotenoid biosynthesis pathway showed common pattern across five cultivars with higher expression at 8 and/or 16 DPA then dropped considerably at 24 and 32 DPA. Almost all genes were up-regulated in CDC Jade cultivar. Correlation analysis between gene expression and carotenoid concentration showed that the genes involved in the primary step of carotenoid biosynthesis pathway including carotenoid desaturase and isomerase positively correlated with various carotenoid components in chickpea seeds. A negative correlation was found between hydroxylation activity and provitamin A concentration in the seeds. The highest provitamin A concentration including β-carotene and β-cryptoxanthin were found in green cotyledon chickpea cultivars.
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Abdel-Ghani AH, Kumar B, Pace J, Jansen C, Gonzalez-Portilla PJ, Reyes-Matamoros J, San Martin JP, Lee M, Lübberstedt T. Association analysis of genes involved in maize (Zea mays L.) root development with seedling and agronomic traits under contrasting nitrogen levels. PLANT MOLECULAR BIOLOGY 2015; 88:133-147. [PMID: 25840559 DOI: 10.1007/s11103-015-0314-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/28/2015] [Indexed: 06/04/2023]
Abstract
A better understanding of the genetic control of root development might allow one to develop lines with root systems with the potential to adapt to soils with limited nutrient availability. For this purpose, an association study (AS) panel consisting of 74 diverse set of inbred maize lines were screened for seedling root traits and adult plant root traits under two contrasting nitrogen (N) levels (low and high N). Allele re-sequencing of RTCL, RTH3, RUM1, and RUL1 genes related to root development was carried out for AS panel lines. Association analysis was carried out between individual polymorphisms, and both seedling and adult plant traits, while controlling for spurious associations due to population structure and kinship relations. Based on the SNPs identified in RTCL, RTH3, RUM1, and RUL1, lines within the AS panel were grouped into 16, 9, 22, and 7 haplotypes, respectively. Association analysis revealed several polymorphisms within root genes putatively associated with the variability in seedling root and adult plant traits development under contrasting N levels. The highest number of significantly associated SNPs with seedling root traits were found in RTCL (19 SNPs) followed by RUM1 (4 SNPs) and in case of RTH3 and RUL1, two and three SNPs, respectively, were significantly associated with root traits. RTCL and RTH3 were also found to be associated with grain yield. Thus considerable allelic diversity is present within the candidate genes studied and can be utilized to develop functional markers that allow identification of maize lines with improved root architecture and yield under N stress conditions.
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Affiliation(s)
- Adel H Abdel-Ghani
- Department of Plant Production, Faculty of Agriculture, Mu'tah University, P.O. Box 7, Karak, Jordan,
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Yan S, Sun D, Sun G. Genetic divergence in domesticated and non-domesticated gene regions of barley chromosomes. PLoS One 2015; 10:e0121106. [PMID: 25812037 PMCID: PMC4374956 DOI: 10.1371/journal.pone.0121106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/11/2015] [Indexed: 11/18/2022] Open
Abstract
Little is known about the genetic divergence in the chromosomal regions with domesticated and non-domesticated genes. The objective of our study is to examine the effect of natural selection on shaping genetic diversity of chromosome region with domesticated and non-domesticated genes in barley using 110 SSR markers. Comparison of the genetic diversity loss between wild and cultivated barley for each chromosome showed that chromosome 5H had the highest divergence of 35.29%, followed by 3H, 7H, 4H, 2H, 6H. Diversity ratio was calculated as (diversity of wild type – diversity of cultivated type)/diversity of wild type×100%. It was found that diversity ratios of the domesticated regions on 5H, 1H and 7H were higher than those of non-domesticated regions. Diversity ratio of the domesticated region on 2H and 4H is similar to that of non-domesticated region. However, diversity ratio of the domesticated region on 3H is lower than that of non-domesticated region. Averaged diversity among six chromosomes in domesticated region was 33.73% difference between wild and cultivated barley, and was 27.56% difference in the non-domesticated region. The outcome of this study advances our understanding of the evolution of crop chromosomes.
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Affiliation(s)
- Songxian Yan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- * E-mail: (DS); . (GS)
| | - Genlou Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Biology, Saint Mary’s University, Halifax, Nova Scotia, B3H 3C3, Canada
- * E-mail: (DS); . (GS)
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Kumar B, Talukdar A, Verma K, Bala I, Harish GD, Gowda S, Lal SK, Sapra RL, Singh KP. Mapping of yellow mosaic virus (YMV) resistance in soybean (Glycine max L. Merr.) through association mapping approach. Genetica 2015; 143:1-10. [PMID: 25475043 DOI: 10.1007/s10709-014-9801-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 11/22/2014] [Indexed: 10/24/2022]
Abstract
Yellow Mosaic Virus (YMV) is a serious disease of soybean. Resistance to YMV was mapped in 180 soybean genotypes through association mapping approach using 121 simple sequence repeats (SSR) and four resistance gene analogue (RGA)-based markers. The association mapping population (AMP) (96 genotypes) and confirmation population (CP) (84 genotypes) was tested for resistance to YMV at hot-spot consecutively for 3 years (2007-2009). The genotypes exhibited significant variability for YMV resistance (P < 0.01). Molecular genotyping and population structure analysis with 'admixture' co-ancestry model detected seven optimal sub-populations in the AMP. Linkage disequilibrium (LD) between the markers extended up to 35 and 10 cM with r2 > 0.15, and >0.25, respectively. The 4 RGA-based markers showed no association with YMV resistance. Two SSR markers, Satt301 and GMHSP179 on chromosome 17 were found to be in significant LD with YMV resistance. Contingency Chi-square test confirmed the association (P < 0.01) and the utility of the markers was validated in the CP. It would pave the way for marker assisted selection for YMV resistance in soybean. This is the first report of its kind in soybean.
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Affiliation(s)
- Bhupender Kumar
- Cummings's Lab., Directorate of Maize Research, Pusa Campus, New Delhi, 12, India
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Kumar B, Talukdar A, Bala I, Verma K, Lal SK, Sapra RL, Namita B, Chander S, Tiwari R. Population structure and association mapping studies for important agronomic traits in soybean. J Genet 2014; 93:775-84. [PMID: 25572236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The present study was carried out with a set of 96 diverse soybean genotypes with the objectives of analysing the population structure and to identify molecular markers associated with important agronomic traits. Large phenotypic variability was observed for the agronomic traits under study indicating suitability of the genotypes for association studies. The maximum values for plant height, pods per plant, seeds per pod, 100-seed weight and seed yield per plant were approximately two and half to three times more than the minimum values for the genotypes. Seed yield per plant was found to be significantly correlated with pods per plant (r = 0.77), 100-seed weight (r = 0.35) and days to maturity (r = 0.23). The population structure studies depicted the presence of seven subpopulations which nearly corresponded with the source of geographical origin of the genotypes. Linkage disequilibrium (LD) between the linked markers decreased with the increased distance, and a substantial drop in LD decay values was observed between 30 and 35 cM. Genomewide marker-traits association analysis carried out using general linear (GLM) and mixed linear models (MLM) identified six genomic regions (two of them were common in both) on chromosomes 6, 7, 8, 13, 15 and 17, which were found to be significantly associated with various important traits viz., plant height, pods per plant, 100-seed weight, plant growth habit, average number of seeds per pod, days to 50% flowering and days to maturity. The phenotypic variation explained by these loci ranged from 6.09 to 13.18% and 4.25 to 9.01% in the GLM and MLM studies, respectively. In conclusion, association mapping (AM) in soybean could be a viable alternative to conventional QTL mapping approach.
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Affiliation(s)
- Bhupender Kumar
- Cummings's Laboratory, Directorate of Maize Research, Pusa Campus, New Delhi 110 012, India.
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Giuliano G. Plant carotenoids: genomics meets multi-gene engineering. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:111-7. [PMID: 24912125 DOI: 10.1016/j.pbi.2014.05.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/30/2014] [Accepted: 05/08/2014] [Indexed: 05/03/2023]
Abstract
Carotenoids are present in plant photosynthetic tissues, where they have essential roles in photoreception and photoprotection, as well as in non-photosynthetic tissues, where they act as colorants, precursors for plant isoprenoid volatiles and signaling molecules (abscisic acid and strigolactones), nutritional antioxidants and vitamin A precursors. This review presents the recent advances in our understanding of their biosynthesis, the key metabolic steps controlling their accumulation in plant non-photosynthetic tissues and their metabolic engineering using multi-gene approaches.
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Affiliation(s)
- Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Research Center, Via Anguillarese 301, Roma 00123, Italy.
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Adetunji I, Willems G, Tschoep H, Bürkholz A, Barnes S, Boer M, Malosetti M, Horemans S, van Eeuwijk F. Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:559-571. [PMID: 24292512 DOI: 10.1007/s00122-013-2239-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 11/20/2013] [Indexed: 06/02/2023]
Abstract
Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection. Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after <6 cM on all chromosomes in both pools. In the wild beet accessions, there was a strong LD decay: on average LD disappeared after 1 cM when LD was calculated with a correction for genetic relatedness. Persistence of LD was not only observed between distant SNPs on the same chromosome, but also between SNPs on different chromosomes. Regions on chromosomes 3 and 4 that harbor disease resistance and monogermy loci showed strong genetic differentiation between the pollen and seed parent pools. Other regions, on chromosomes 8 and 9, for which no a priori information was available with respect to their contribution to the phenotype, still contributed to clustering of lines in the elite breeding material.
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Meyer RS, Purugganan MD. Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 2014; 14:840-52. [PMID: 24240513 DOI: 10.1038/nrg3605] [Citation(s) in RCA: 592] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.
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Affiliation(s)
- Rachel S Meyer
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place, New York University, New York 10003, USA
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Thirunavukkarasu N, Hossain F, Shiriga K, Mittal S, Arora K, Rathore A, Mohan S, Shah T, Sharma R, Namratha PM, Mithra ASV, Mohapatra T, Gupta HS. Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs. BMC Genomics 2013; 14:877. [PMID: 24330649 PMCID: PMC3867671 DOI: 10.1186/1471-2164-14-877] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 12/10/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Maize is an increasingly important food crop in southeast Asia. The elucidation of its genetic architecture, accomplished by exploring quantitative trait loci and useful alleles in various lines across numerous breeding programs, is therefore of great interest. The present study aimed to characterize subtropical maize lines using high-quality SNPs distributed throughout the genome. RESULTS We genotyped a panel of 240 subtropical elite maize inbred lines and carried out linkage disequilibrium, genetic diversity, population structure, and principal component analyses on the generated SNP data. The mean SNP distance across the genome was 70 Kb. The genome had both high and low linkage disequilibrium (LD) regions; the latter were dominant in areas near the gene-rich telomeric portions where recombination is frequent. A total of 252 haplotype blocks, ranging in size from 1 to 15.8 Mb, were identified. Slow LD decay (200-300 Kb) at r(2) ≤ 0.1 across all chromosomes explained the selection of favorable traits around low LD regions in different breeding programs. The association mapping panel was characterized by strong population substructure. Genotypes were grouped into three distinct clusters with a mean genetic dissimilarity coefficient of 0.36. CONCLUSIONS The genotyped panel of subtropical maize lines characterized in this study should be useful for association mapping of agronomically important genes. The dissimilarity uncovered among genotypes provides an opportunity to exploit the heterotic potential of subtropical elite maize breeding lines.
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Huang Q, Lattorff HMG, Kryger P, Le Conte Y, Moritz RFA. A selective sweep in a microsporidian parasiteNosema-tolerant honeybee population,Apis mellifera. Anim Genet 2013; 45:267-73. [DOI: 10.1111/age.12114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Q. Huang
- Institut für Biologie/Zoologie, Molekulare Ökologie; Martin-Luther-Universität Halle -Wittenberg; Hoher Weg 4 06099 Halle (Saale) Germany
- Honeybee Research Institute; Jiangxi Agricultural University; 330045 Nanchang China
| | - H. M. G. Lattorff
- Institut für Biologie/Zoologie, Molekulare Ökologie; Martin-Luther-Universität Halle -Wittenberg; Hoher Weg 4 06099 Halle (Saale) Germany
- German Institute for Integrative Biodiversity Research (iDiv); Bio City 04103 Leipzig Germany
| | - P. Kryger
- Department of Agroecology; Section of Entomology and Plantpathology; Aarhus University; Flakkebjerg 4200 Slagelse Denmark
| | - Y. Le Conte
- INRA; UMR 406 Ecologie des Invertébrés; Site Agroparc 84914 Avignon Cedex 9 France
| | - R. F. A. Moritz
- Institut für Biologie/Zoologie, Molekulare Ökologie; Martin-Luther-Universität Halle -Wittenberg; Hoher Weg 4 06099 Halle (Saale) Germany
- German Institute for Integrative Biodiversity Research (iDiv); Bio City 04103 Leipzig Germany
- RoBeeTech; Universitatea de Stiinte Agricole si Medicina Vetereinaria Cluj-Napoca; 400372 Cluj-Napoca Romania
- Department of Zoology and Entomology; University of Pretoria; Pretoria 0002 South Africa
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Evans J, McCormick RF, Morishige D, Olson SN, Weers B, Hilley J, Klein P, Rooney W, Mullet J. Extensive variation in the density and distribution of DNA polymorphism in sorghum genomes. PLoS One 2013; 8:e79192. [PMID: 24265758 PMCID: PMC3827139 DOI: 10.1371/journal.pone.0079192] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 09/24/2013] [Indexed: 11/25/2022] Open
Abstract
Sorghum genotypes currently used for grain production in the United States were developed from African landraces that were imported starting in the mid-to-late 19th century. Farmers and plant breeders selected genotypes for grain production with reduced plant height, early flowering, increased grain yield, adaptation to drought, and improved resistance to lodging, diseases and pests. DNA polymorphisms that distinguish three historically important grain sorghum genotypes, BTx623, BTx642 and Tx7000, were characterized by genome sequencing, genotyping by sequencing, genetic mapping, and pedigree-based haplotype analysis. The distribution and density of DNA polymorphisms in the sequenced genomes varied widely, in part because the lines were derived through breeding and selection from diverse Kafir, Durra, and Caudatum race accessions. Genomic DNA spanning dw1 (SBI-09) and dw3 (SBI-07) had identical haplotypes due to selection for reduced height. Lower SNP density in genes located in pericentromeric regions compared with genes located in euchromatic regions is consistent with background selection in these regions of low recombination. SNP density was higher in euchromatic DNA and varied >100-fold in contiguous intervals that spanned up to 300 Kbp. The localized variation in DNA polymorphism density occurred throughout euchromatic regions where recombination is elevated, however, polymorphism density was not correlated with gene density or DNA methylation. Overall, sorghum chromosomes contain distal euchromatic regions characterized by extensive, localized variation in DNA polymorphism density, and large pericentromeric regions of low gene density, diversity, and recombination.
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Affiliation(s)
- Joseph Evans
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Ryan F. McCormick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Daryl Morishige
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Sara N. Olson
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Brock Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Josie Hilley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Patricia Klein
- Department of Horticulture, Texas A&M University, College Station, Texas, United States of America
| | - William Rooney
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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