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Gaur VS, Sood S, Guzmán C, Olsen KM. Molecular insights on the origin and development of waxy genotypes in major crop plants. Brief Funct Genomics 2024; 23:193-213. [PMID: 38751352 DOI: 10.1093/bfgp/elad035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 06/14/2024] Open
Abstract
Starch is a significant ingredient of the seed endosperm with commercial importance in food and industry. Crop varieties with glutinous (waxy) grain characteristics, i.e. starch with high amylopectin and low amylose, hold longstanding cultural importance in some world regions and unique properties for industrial manufacture. The waxy character in many crop species is regulated by a single gene known as GBSSI (or waxy), which encodes the enzyme Granule Bound Starch Synthase1 with null or reduced activity. Several allelic variants of the waxy gene that contribute to varying levels of amylose content have been reported in different crop plants. Phylogenetic analysis of protein sequences and the genomic DNA encoding GBSSI of major cereals and recently sequenced millets and pseudo-cereals have shown that GBSSI orthologs form distinct clusters, each representing a separate crop lineage. With the rapidly increasing demand for waxy starch in food and non-food applications, conventional crop breeding techniques and modern crop improvement technologies such as gene silencing and genome editing have been deployed to develop new waxy crop cultivars. The advances in research on waxy alleles across different crops have unveiled new possibilities for modifying the synthesis of amylose and amylopectin starch, leading to the potential creation of customized crops in the future. This article presents molecular lines of evidence on the emergence of waxy genes in various crops, including their genesis and evolution, molecular structure, comparative analysis and breeding innovations.
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Affiliation(s)
- Vikram S Gaur
- Raja Bhoj College of Agriculture, Balaghat, JNKVV, Jabalpur, Madhya Pradesh, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla- 171001, Himachal Pradesh, India
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, CeiA3, ES-14071, Córdoba, Spain
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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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Guo N, Tang S, Wang Y, Chen W, An R, Ren Z, Hu S, Tang S, Wei X, Shao G, Jiao G, Xie L, Wang L, Chen Y, Zhao F, Sheng Z, Hu P. A mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice. Nat Commun 2024; 15:1134. [PMID: 38326370 PMCID: PMC10850359 DOI: 10.1038/s41467-024-45402-z] [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: 11/27/2022] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Preharvest sprouting (PHS) is a deleterious phenotype that occurs frequently in rice-growing regions where the temperature and precipitation are high. It negatively affects yield, quality, and downstream grain processing. Seed dormancy is a trait related to PHS. Longer seed dormancy is preferred for rice production as it can prevent PHS. Here, we map QTLs associated with rice seed dormancy and clone Seed Dormancy 3.1 (SDR3.1) underlying one major QTL. SDR3.1 encodes a mediator of OsbZIP46 deactivation and degradation (MODD). We show that SDR3.1 negatively regulates seed dormancy by inhibiting the transcriptional activity of ABIs. In addition, we reveal two critical amino acids of SDR3.1 that are critical for the differences in seed dormancy between the Xian/indica and Geng/japonica cultivars. Further, SDR3.1 has been artificially selected during rice domestication. We propose a two-line model for the process of rice seed dormancy domestication from wild rice to modern cultivars. We believe the candidate gene and germplasm studied in this study would be beneficial for the genetic improvement of rice seed dormancy.
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Affiliation(s)
- Naihui Guo
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China
| | - Shengjia Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yakun Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- National Nanfan Research Academy (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, P. R. China
| | - Wei Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ruihu An
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zongliang Ren
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shikai Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Guiai Jiao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Lihong Xie
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ling Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ying Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Fengli Zhao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Jiangxi Early-season Rice Research Center, Pingxiang, Jiangxi Province, 337000, P. R. China.
| | - Peisong Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China.
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4
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Brown KE, Koenig D. On the hidden temporal dynamics of plant adaptation. CURRENT OPINION IN PLANT BIOLOGY 2022; 70:102298. [PMID: 36126489 DOI: 10.1016/j.pbi.2022.102298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 07/28/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Adaptation to a wide range of environments is a major driver of plant diversity. It is now possible to catalog millions of potential adaptive genomic differences segregating between environments within a plant species in a single experiment. Understanding which of these changes contributes to adaptive phenotypic divergence between plant populations is a major goal of evolutionary biologists and crop breeders. In this review, we briefly highlight the approaches frequently used to understand the genetic basis of adaptive phenotypes in plants, and we discuss some of the limitations of these methods. We propose that direct observation of the process of adaptation using multigenerational studies and whole genome sequencing is a crucial missing component of recent studies of plant adaptation because it complements several shortcomings of sampling-based techniques.
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Affiliation(s)
- Keely E Brown
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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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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Wang M, Chen J, Zhou F, Yuan J, Chen L, Wu R, Liu Y, Zhang Q. The ties of brotherhood between japonica and indica rice for regional adaptation. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1369-1379. [PMID: 34902099 DOI: 10.1007/s11427-021-2019-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
Selection of beneficial genomic variants was crucial for regional adaptation of crops during domestication, but the underlying genomic basis remains largely unexplored. Here we report a genome-wide selective-sweep analysis of 655 japonica and 1,205 indica accessions selected from 2,673 landraces through principal component analysis to identify 5,636 non-synonymous single nucleotide polymorphisms (SNPs) fixed in at least one subspecies. We classified these SNPs into three groups, jiS (japonica- and indica-selected), jS (japonica-selected only), and iS (indica-selected only), and documented evidence for selection acting on these groups, their relation to yield-related traits, such as heading date, and their practical value in cropping area prediction. We also demonstrated the role of a jiS-SNP-containing gene in temperature adaptability. Our study informs genes underpinning adaptation that may shape Green Super Rice and proposes a time-saving, cost-reducing selection strategy of genomic breeding, sweep-SNP-guided selection, for developing regionally-adapted heterosis.
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Affiliation(s)
- Man Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jiehu Chen
- Science Corporation of Gene, Guangzhou, 510000, China
| | - Feng Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jianming Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Libin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Rongling Wu
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- SCAU Main Campus Teaching & Research Base, Guangzhou, 510642, China.
| | - Qunyu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- SCAU Main Campus Teaching & Research Base, Guangzhou, 510642, China.
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Li J, Zhang Y, Ma R, Huang W, Hou J, Fang C, Wang L, Yuan Z, Sun Q, Dong X, Hou Y, Wang Y, Kong F, Sun L. Identification of ST1 reveals a selection involving hitchhiking of seed morphology and oil content during soybean domestication. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1110-1121. [PMID: 35178867 PMCID: PMC9129076 DOI: 10.1111/pbi.13791] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/29/2021] [Accepted: 01/26/2022] [Indexed: 05/26/2023]
Abstract
Seed morphology and quality of cultivated soybean (Glycine max) have changed dramatically during domestication from their wild relatives, but their relationship to selection is poorly understood. Here, we describe a semi-dominant locus, ST1 (Seed Thickness 1), affecting seed thickness and encoding a UDP-D-glucuronate 4-epimerase, which catalyses UDP-galacturonic acid production and promotes pectin biosynthesis. Interestingly, this morphological change concurrently boosted seed oil content, which, along with up-regulation of glycolysis biosynthesis modulated by ST1, enabled soybean to become a staple oil crop. Strikingly, ST1 and an inversion controlling seed coat colour formed part of a single selective sweep. Structural variation analysis of the region surrounding ST1 shows that the critical mutation in ST1 existed in earlier wild relatives of soybean and the region containing ST1 subsequently underwent an inversion, which was followed by successive selection for both traits through hitchhiking during selection for seed coat colour. Together, these results provide direct evidence that simultaneously variation for seed morphology and quality occurred earlier than variation for seed coat colour during soybean domestication. The identification of ST1 thus sheds light on a crucial phase of human empirical selection in soybeans and provides evidence that our ancestors improved soybean based on taste.
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Affiliation(s)
- Jun Li
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yuhang Zhang
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Ruirui Ma
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Wenxuan Huang
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jingjing Hou
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Chao Fang
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Lingshuang Wang
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Zhihui Yuan
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Qun Sun
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xuehui Dong
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yufeng Hou
- College of Humanities and Development StudiesChina Agricultural UniversityBeijingChina
| | - Ying Wang
- College of Plant ScienceJilin UniversityChangchunChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Lianjun Sun
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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Jiang C, Rashid MAR, Zhang Y, Zhao Y, Pan Y. Genome wide association study on development and evolution of glutinous rice. BMC Genom Data 2022; 23:33. [PMID: 35508973 PMCID: PMC9066796 DOI: 10.1186/s12863-022-01033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glutinous rice as a special endosperm type is consumed as a staple food in East Asian countries by consumers' preference. Genetic studies on glutinous rice could be conducive to improve rice quality and understand its development and evolution. Therefor, we sought to explore more genes related to glutinous by genome wide association study and research the formation history for glutinous. RESULTS Here, genome-wide association study was performed to explore the associated loci/genes underlying glutinous rice by using 2108 rice accessions. Combining the expression patterns analysis, 127, 81, and 48 candidate genes were identified to be associated with endosperm type in whole rice panel, indica, and japonica sub-populations. There were 32 genes, including three starch synthesis-related genes Wx, SSG6, and OsSSIIa, detected simultaneously in the whole rice panel and subpopulations, playing important role in determining glutinous rice. The combined haplotype analyses revealed that the waxy haplotypes combination of three genes mainly distributed in Southeast Asia (SEA), SEA islands (SER) and East Asia islands (EAR). Through population structure and genetic differentiation, we suggest that waxy haplotypes of the three genes firstly evolved or were directly inherited from wild rice in japonica, and then introgressed into indica in SER, SEA and EAR. CONCLUSIONS The cloning and natural variation analysis of waxy-related genes are of great significance for the genetic improvement of quality breeding and comprehend the history in glutinous rice. This work provides valuable information for further gene discovery and understanding the evolution and formation for glutinous rice in SEA, SER and EAR.
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Affiliation(s)
- Conghui Jiang
- Shandong Rice Engineering Technology Research Center, Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Muhammad Abdul Rehman Rashid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Yanhong Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China.
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China.
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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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10
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Lu Y, Xu Y, Li N. Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies. RICE (NEW YORK, N.Y.) 2022; 15:11. [PMID: 35166949 PMCID: PMC8847465 DOI: 10.1186/s12284-022-00556-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/22/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Asian rice (Oryza sativa L.) has been a model plant but its cultivation history is inadequately understood, and its origin still under debate. Several enigmas remain, including how this annual crop shifted its growth habit from its perennial ancestor, O. rufipogon, why genetic divergence between indica and japonica appears older than the history of human domestication, and why some domestication genes do not show signals of introgression between subgroups. Addressing these issues may benefit both basic research and rice breeding. RESULTS Gene genealogy-based mutation (GGM) analysis shows that history of Asian rice is divided into two phases (Phase I and II) of about equal lengths. Mutations occurred earlier than the partition of indica and japonica to Os genome mark Phase-I period. We diagnosed 91 such mutations among 101 genes sampled across 12 chromosomes of Asian rice and its wild relatives. Positive selection, detected more at 5' regions than at coding regions of some of the genes, involved 22 loci (e.g., An-1, SH4, Rc, Hd3a, GL3.2, OsMYB3, OsDFR, and OsMYB15), which affected traits from easy harvesting, grain color, flowering time, productivity, to likely taste and tolerance. Phase-I mutations of OsMYB3, OsHd3a and OsDFR were experimentally tested and all caused enhanced functions of the genes in vivo. Phase-II period features separate cultivations, lineage-specific selection, and expanded domestication to more genes. Further genomic analysis, along with phenotypic comparisons, indicates that O. sativa is hybrid progeny of O. rufipogon and O. nivara, inherited slightly more genes of O. rufipogon. Congruently, modern alleles of the sampled genes are approximately 6% ancient, 38% uni-specific, 40% bi-specific (mixed), and 15% new after accumulating significant mutations. Results of sequencing surveys across modern cultivars/landraces indicate locus-specific usages of various alleles while confirming the associated mutations. CONCLUSIONS Asian rice was initially domesticated as one crop and later separate selection mediated by human resulted in its major subgroups. This history and the hybrid origin well explain previous puzzles. Positive selection, particularly in 5' regions, was the major force underlying trait domestication. Locus-specific domestication can be characterized and the result may facilitate breeders in developing better rice varieties in future.
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Affiliation(s)
- Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Present Address: College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016 China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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11
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Semagn K, Iqbal M, Alachiotis N, N'Diaye A, Pozniak C, Spaner D. Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array. Sci Rep 2021; 11:23773. [PMID: 34893626 PMCID: PMC8664822 DOI: 10.1038/s41598-021-02666-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Previous molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20-40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Muhammad Iqbal
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Nikolaos Alachiotis
- Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, 3230, Enschede, OV, The Netherlands
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Zhang G, Wang R, Ma J, Gao H, Deng L, Wang N, Wang Y, Zhang J, Li K, Zhang W, Mu F, Liu H, Wang Y. Genome-wide association studies of yield-related traits in high-latitude japonica rice. BMC Genom Data 2021; 22:39. [PMID: 34610789 PMCID: PMC8493688 DOI: 10.1186/s12863-021-00995-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heilongjiang Province is a high-quality japonica rice cultivation area in China. One in ten bowls of Chinese rice is produced here. Increasing yield is one of the main aims of rice production in this area. However, yield is a complex quantitative trait composed of many factors. The purpose of this study was to determine how many genetic loci are associated with yield-related traits. Genome-wide association studies (GWAS) were performed on 450 accessions collected from northeast Asia, including Russia, Korea, Japan and Heilongjiang Province of China. These accessions consist of elite varieties and landraces introduced into Heilongjiang Province decade ago. RESULTS After resequencing of the 450 accessions, 189,019 single nucleotide polymorphisms (SNPs) were used for association studies by two different models, a general linear model (GLM) and a mixed linear model (MLM), examining four traits: days to heading (DH), plant height (PH), panicle weight (PW) and tiller number (TI). Over 25 SNPs were found to be associated with each trait. Among them, 22 SNPs were selected to identify candidate genes, and 2, 8, 1 and 11 SNPs were found to be located in 3' UTR region, intron region, coding region and intergenic region, respectively. CONCLUSIONS All SNPs detected in this research may become candidates for further fine mapping and may be used in the molecular breeding of high-latitude rice.
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Affiliation(s)
- Guomin Zhang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Rongsheng Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Juntao Ma
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Hongru Gao
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Lingwei Deng
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Nanbo Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Yongli Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Jun Zhang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Kun Li
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Wei Zhang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Fengchen Mu
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Hui Liu
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Ying Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China.
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China.
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Maung TZ, Chu SH, Park YJ. Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II ( GBSSII) Gene in Korean Rice Accessions (KRICE_CORE). Foods 2021; 10:2359. [PMID: 34681408 PMCID: PMC8535093 DOI: 10.3390/foods10102359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022] Open
Abstract
Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1-C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima's D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima's D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
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KHARSHIING GAYLE, CHRUNGOO NIKHILK. Wx alleles in rice: relationship with apparent amylose content of starch and a possible role in rice domestication. J Genet 2021. [DOI: 10.1007/s12041-021-01311-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Maung TZ, Yoo JM, Chu SH, Kim KW, Chung IM, Park YJ. Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:707237. [PMID: 34504507 PMCID: PMC8421862 DOI: 10.3389/fpls.2021.707237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Granule-bound starch synthase I (GBSSI) is responsible for Waxy gene encoding the, which is involved in the amylose synthesis step of starch biosynthesis. We investigated the genotypic and haplotypic variations of GBSSI (Os06g0133000) gene, including its evolutionary relatedness in the nucleotide sequence level using single-nucleotide polymorphisms (SNPs), indels, and structural variations (SVs) from 475 Korean World Rice Collection (KRICE_CORE), which comprised 54 wild rice and 421 cultivated represented by 6 ecotypes (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture) or in another way by 3 varietal types (landrace, weedy, and bred). The results revealed that 27 of 59 haplotypes indicated a total of 12 functional SNPs (fSNPs), identifying 9 novel fSNPs. According to the identified novel fSNPs, we classified the entire rice collection into three groups: cultivated, wild, and mixed (cultivated and wild) rice. Five novel fSNPs were localized in wild rice: four G/A fSNPs in exons 2, 9, and 12 and one T/C fSNP in exon 13. We also identified the three previously reported fSNPs, namely, a G/A fSNP (exon 4), an A/C fSNP (exon 6), and a C/T fSNP (exon 10), which were observed only in cultivated rice, whereas an A/G fSNP (exon 4) was observed exclusively in wild rice. All-against-all comparison of four varietal types or six ecotypes of cultivated rice with wild rice showed that the GBSSI diversity was higher only in wild rice (π = 0.0056). The diversity reduction in cultivated rice can be useful to encompass the origin of this gene GBSSI during its evolution. Significant deviations of positive (wild and indica under balancing selection) and negative (temperate and tropical japonica under purifying selection) Tajima's D values from a neutral model can be informative about the selective sweeps of GBSSI genome insights. Despite the estimation of the differences in population structure and principal component analysis (PCA) between wild and subdivided cultivated subgroups, an inbreeding effect was quantified by F ST statistic, signifying the genetic relatedness of GBSSI. Our findings of a novel wild fSNPS can be applicable for future breeding of waxy rice varieties. Furthermore, the signatures of selective sweep can also be of informative into further deeper insights during domestication.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Ji-Min Yoo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Kyu-Won Kim
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Ill-Min Chung
- Department of Applied Life Science, Konkuk University, Seoul, South Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
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16
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Could Japonica Rice Be an Alternative Variety for Increased Global Food Security and Climate Change Mitigation? Foods 2021; 10:foods10081869. [PMID: 34441646 PMCID: PMC8393797 DOI: 10.3390/foods10081869] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
The growing importance of rice globally over the past three decades is evident in its strategic place in many countries' food security planning policies. Still, its cultivation emits substantial greenhouse gases (GHGs). The Indica and Japonica sub-species of Oryza sativa L. are mainly grown, with Indica holding the largest market share. The awareness, economics, and acceptability of Japonica rice in a food-insecure Indica rice-consuming population were surveyed. The impact of parboiling on Japonica rice was studied and the factors which most impacted stickiness were investigated through sensory and statistical analyses. A comparison of the growing climate and greenhouse gas emissions of Japonica and Indica rice was carried out by reviewing previous studies. Survey results indicated that non-adhesiveness and pleasant aroma were the most preferred properties. Parboiling treatment altered Japonica rice's physical and chemical properties, introducing gelatinization of starch and reducing adhesiveness while retaining micronutrient concentrations. Regions with high food insecurity and high consumption of Indica rice were found to have suitable climatic conditions for growing Japonica rice. Adopting the higher-yielding, nutritious Japonica rice whose cultivation emits less GHG in these regions could help strengthen food security while reducing GHGs in global rice cultivation.
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17
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El Sayed MA, Kheir AM, Hussein FA, Ali EF, Selim ME, Majrashi A, El Shamey EA. Developing new lines of Japonica rice for higher quality and yield under arid conditions. PeerJ 2021; 9:e11592. [PMID: 34178464 PMCID: PMC8210806 DOI: 10.7717/peerj.11592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/20/2021] [Indexed: 11/24/2022] Open
Abstract
Rice is the world's largest food crop, and its production needs to be doubled by 2050 to cope with population growth and associated demand. In addition to the value of improving yields, quality is also important for breeders and consumers, but it pays less attention in arid regions. During two successive summer growing seasons, the experimental material focused on 34 genotypes developed from different crosses on Fn generation after fixation as well as six of the most recent commercial cultivars used for comparisons. The results showed that a high yield of grain followed by high milling and grain quality characteristics were observed among the 34 genotypes used in this analysis. Highly important and positive correlations between the percentage of hulling and the percentage of milling (0.424) and the yield ability could be accomplished by choosing the number of panicles per plant and the weight of the panicles. Selection criteria for good quality should be met by the percentage of head rice and many mineral elements, particularly zinc and iron. As a consequence, the genotypes M.J 5460S/SK105-1, M.J 5460S/GZ7768-1, M.J 5460S/G177-1, M.J 5460S/SK105-3 and M.J 5460S/SK106-4 had desirable high yield and quality characteristics and could be used as promising accessions to the rice breeding program in arid regions. In addition to commercial genotypes, improved Japonica rice genotypes could be produced in arid conditions for higher yield and quality, leading to an increase in total production, supporting food security and nutrition.
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Affiliation(s)
- Mahmoud A.A. El Sayed
- Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Egypt
| | - Ahmed M.S. Kheir
- Soils, Water and Environment Research Institute, Agriculture Research Centre, Egypt
| | - Fatma A. Hussein
- Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Egypt
| | - Esmat F. Ali
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Mahmoud E. Selim
- Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Egypt
| | - Ali Majrashi
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Essam A.Z. El Shamey
- Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Egypt
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18
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Wedger MJ, Schumann AC, Gross BL. Candidate genes and signatures of directional selection on fruit quality traits during apple domestication. AMERICAN JOURNAL OF BOTANY 2021; 108:616-627. [PMID: 33837962 DOI: 10.1002/ajb2.1636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
PREMISE During plant domestication, traits can be subject to a variety of types of selection, ranging from strong directional selection for traits such as seed or fruit size to diversifying selection for traits like color or flavor. These types of selection interact with other evolutionary processes including genetic bottlenecks and interspecific gene flow to generate different levels of genetic diversity across the genome and at target genes in domesticated lineages, but little is known about the impacts of these processes in perennial fruit crops. METHODS We used sequence capture by hybridization to examine patterns of diversity at a suite of candidate domestication and anonymous background genes in domesticated apple (Malus ×domestica) in comparison to its wild relatives Malus sieversii and Malus orientalis. RESULTS We found no change in average diversity at these candidate domestication genes across the three species. However, a subset of the genes did exhibit patterns of very high or very low diversity in M. ×domestica compared to its progenitor, M. sieversii. Of the genes with characterized function, the low-diversity genes mainly contributed to fruit quality traits like color and flavor, predicted to be under conscious, directional selection relatively late in the domestication process, while the high-diversity genes included a variety of functions. CONCLUSIONS Overall, these results are consistent with predictions based on the likely timing and nature of selection during domestication and open new avenues for understanding genes with high diversity in a perennial crop compared to its wild relatives.
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Affiliation(s)
- Marshall J Wedger
- Department of Biology, Washington University, Campus Box 1137, St. Louis, MO, 63130, USA
| | - Abby C Schumann
- Minnesota Poultry Testing Laboratory, P.O. Box 126, 622 Bus. Hwy 71 NE, Wilmar, MN, 56201, USA
| | - Briana L Gross
- Department of Biology, University of Minnesota Duluth, 207 Swenson Science Building, 1035 Kirby Drive, Duluth, MN, 55812, USA
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19
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Landini A, Yu S, Gnecchi‐Ruscone GA, Abondio P, Ojeda‐Granados C, Sarno S, De Fanti S, Gentilini D, Di Blasio AM, Jin H, Nguyen TT, Romeo G, Prata C, Bortolini E, Luiselli D, Pettener D, Sazzini M. Genomic adaptations to cereal-based diets contribute to mitigate metabolic risk in some human populations of East Asian ancestry. Evol Appl 2021; 14:297-313. [PMID: 33664777 PMCID: PMC7896717 DOI: 10.1111/eva.13090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 07/20/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
Adoption of diets based on some cereals, especially on rice, signified an iconic change in nutritional habits for many Asian populations and a relevant challenge for their capability to maintain glucose homeostasis. Indeed, rice shows the highest carbohydrates content and glycemic index among the domesticated cereals and its usual ingestion represents a potential risk factor for developing insulin resistance and related metabolic diseases. Nevertheless, type 2 diabetes and obesity epidemiological patterns differ among Asian populations that rely on rice as a staple food, with higher diabetes prevalence and increased levels of central adiposity observed in people of South Asian ancestry rather than in East Asians. This may be at least partly due to the fact that populations from East Asian regions where wild rice or other cereals such as millet have been already consumed before their cultivation and/or were early domesticated have relied on these nutritional resources for a period long enough to have possibly evolved biological adaptations that counteract their detrimental side effects. To test such a hypothesis, we compared adaptive evolution of these populations with that of control groups from regions where the adoption of cereal-based diets occurred many thousand years later and which were identified from a genome-wide dataset including 2,379 individuals from 124 East Asian and South Asian populations. This revealed selective sweeps and polygenic adaptive mechanisms affecting functional pathways involved in fatty acids metabolism, cholesterol/triglycerides biosynthesis from carbohydrates, regulation of glucose homeostasis, and production of retinoic acid in Chinese Han and Tujia ethnic groups, as well as in people of Korean and Japanese ancestry. Accordingly, long-standing rice- and/or millet-based diets have possibly contributed to trigger the evolution of such biological adaptations, which might represent one of the factors that play a role in mitigating the metabolic risk of these East Asian populations.
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Affiliation(s)
- Arianna Landini
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
- Centre for Global Health ResearchUsher Institute of Population Health Sciences and InformaticsUniversity of EdinburghEdinburghUK
| | - Shaobo Yu
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | | | - Paolo Abondio
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Claudia Ojeda‐Granados
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
- Department of Molecular Biology in MedicineCivil Hospital of Guadalajara “Fray Antonio Alcalde” and Health Sciences CenterUniversity of GuadalajaraGuadalajaraMexico
| | - Stefania Sarno
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Sara De Fanti
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate ChangeUniversity of BolognaBolognaItaly
| | - Davide Gentilini
- Department of Brain and Behavioral SciencesUniversity of PaviaPaviaItaly
- Italian Auxologic Institute IRCCSCusano Milanino, MilanItaly
| | | | - Hanjun Jin
- Department of Biological SciencesCollege of Natural ScienceDankook UniversityCheonanSouth Korea
| | | | - Giovanni Romeo
- Medical Genetics UnitS. Orsola HospitalUniversity of BolognaBolognaItaly
- European School of Genetic MedicineItaly
| | - Cecilia Prata
- Department of Pharmacy and BiotechnologyUniversity of BolognaBolognaItaly
| | | | - Donata Luiselli
- Department of Cultural HeritageUniversity of BolognaRavennaItaly
| | - Davide Pettener
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Marco Sazzini
- Laboratory of Molecular Anthropology & Centre for Genome BiologyDepartment of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate ChangeUniversity of BolognaBolognaItaly
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20
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Segregation distortion: high genetic load suggested by a Chinese shrimp family under high-intensity selection. Sci Rep 2020; 10:21820. [PMID: 33311524 PMCID: PMC7732831 DOI: 10.1038/s41598-020-78389-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 11/17/2020] [Indexed: 11/09/2022] Open
Abstract
Segregation distortion is a common phenomenon found in most genetic mapping studies and is an important resource to dissect the mechanism of action in gene loci that cause deviation. Marine animals possess high genetic diversity and genomic heterozygosity, they therefore are ideal model organisms to study segregation distortion induced by selection. In the present study, we constructed a full-sib family of Fenneropenaeus chinensis and exerted high-intensity selection on 10,000 incipient progenies. 2b-RAD method was employed in remaining 273 individuals to develop genome-wide SNPs for segregating analysis and 41,612 SNPs were developed. 50.77% of 32,229 high-quality representative markers deviated from the expected Mendelian ratio. Results showed that most of these distorted markers (91.57%) were influenced at zygotic level. Heterozygote excess (53.07%) and homozygous deletions (41.96%) may both play an important role, sum of which explained 95.03% of distortion after fertilization. However, further results identified highly probable linkage among deleterious alleles, which may account for a considerable portion of heterozygote excess rather than single locus with heterozygote advantage. Results of this study support a major role of deleterious alleles in genetic load, thus in favor of partial dominance hypothesis. It would also offer necessary recommendations for the formulation of breeding strategy in shrimps.
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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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22
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Kumar A, Daware A, Kumar A, Kumar V, Gopala Krishnan S, Mondal S, Patra BC, Singh AK, Tyagi AK, Parida SK, Thakur JK. Genome-wide analysis of polymorphisms identified domestication-associated long low-diversity region carrying important rice grain size/weight quantitative trait loci. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1525-1547. [PMID: 32432802 DOI: 10.1111/tpj.14845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 05/01/2020] [Accepted: 05/12/2020] [Indexed: 05/02/2023]
Abstract
Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, the genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication-driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504 439 single nucleotide polymorphisms (SNPs) and 78 166 insertion-and-deletion polymorphisms. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to the japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and the top four of these could be validated in mapping a population, suggesting this study as a valuable resource for high-throughput genotyping. A contiguous long low-diversity region (LDR) of approximately 6 Mb carrying a major grain weight quantitative trait loci (harbouring OsTOR gene) was identified on Chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication-related traits, including grain size/weight. The aus population retained more allelic variations in the LDR than the japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from the RiceSzWtBase database.
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Affiliation(s)
- Angad Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Arvind Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Subhasish Mondal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Bhaskar C Patra
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - Ashok K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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23
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Abstract
Domestication is a co-evolutionary process that occurs when wild plants are brought into cultivation by humans, leading to origin of new species and/or differentiated populations that are critical for human survival. Darwin used domesticated species as early models for evolution, highlighting their variation and the key role of selection in species differentiation. Over the last two decades, a growing synthesis of plant genetics, genomics, and archaeobotany has led to challenges to old orthodoxies and the advent of fresh perspectives on how crop domestication and diversification proceed. I discuss four new insights into plant domestication - that in general domestication is a protracted process, that unconscious (natural) selection plays a prominent role, that interspecific hybridization may be an important mechanism for crop species diversification and range expansion, and that similar genes across multiple species underlies parallel/convergent phenotypic evolution between domesticated taxa. Insights into the evolutionary origin and diversification of crop species can help us in developing new varieties (and possibly even new species) to deal with current and future environmental challenges in a sustainable manner.
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Affiliation(s)
- Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place New York University, New York, NY, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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24
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Roy S, Banerjee A, Basak N, Bagchi TB, Mandal NP, Patra BC, Misra AK, Singh SK, Rathi RS, Pattanayak A. Genetic diversity analysis of specialty glutinous and low-amylose rice (Oryza sativa L.) landraces of Assam based on Wx locus and microsatellite diversity. J Biosci 2020. [DOI: 10.1007/s12038-020-00059-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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25
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Seo J, Lee SM, Han JH, Shin NH, Lee YK, Kim B, Chin JH, Koh HJ. Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11050562. [PMID: 32443496 PMCID: PMC7290844 DOI: 10.3390/genes11050562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 01/18/2023] Open
Abstract
The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.
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Affiliation(s)
- Jeonghwan Seo
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - So-Myeong Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Jae-Hyuk Han
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
| | - Na-Hyun Shin
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
| | - Yoon Kyung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - Backki Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
- Correspondence: (J.H.C.); (H.-J.K.)
| | - Hee-Jong Koh
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
- Correspondence: (J.H.C.); (H.-J.K.)
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26
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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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27
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Ali N, Li D, Eltahawy MS, Abdulmajid D, Bux L, Liu E, Dang X, Hong D. Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping. BMC Genet 2020; 21:4. [PMID: 31948408 PMCID: PMC6966888 DOI: 10.1186/s12863-020-0811-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/07/2020] [Indexed: 11/12/2022] Open
Abstract
Background Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population. Results The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg− 1, ranging from 0.22 mg.mg-1 to 0.93 mg.mg− 1, with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg− 1 (RM7309–135 bp on chromosome 9) to 0.45 mg.mg− 1 (RM297–180 bp on chromosome 2). RM297–180 bp showed the largest phenotypic effect value (0.44 mg.mg− 1 in 2016 and 0.45 mg.mg− 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297–175 bp (0.43 mg.mg− 1 in 2016 and 0.44 mg.mg− 1 in 2017). Conclusion Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.
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Affiliation(s)
- Nour Ali
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Laboratory of Crop Production and Multiplication, Field Crops Research Department, Agricultural Faculty, Damascus University, Damascus, Syria.,Laboratory of Crop Genetics and Germplasm Enhancement, Field Crops Research Department, Agricultural Faculty, Damascus University, Damascus, Syria
| | - Dalu Li
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Moaz S Eltahawy
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Agronomy Department, Faculty of Agriculture, Zagazig University, Zagazig, Sharqia, 44519, Egypt
| | - Dina Abdulmajid
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Rice Research and Training Center, Field Crops Research Institute, Agricultural Research Center, Kafr El-Sheikh, 33717, Egypt
| | - Lal Bux
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erbao Liu
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaojing Dang
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Delin Hong
- Nanjing Agricultural University, Nanjing, 210095, China. .,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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28
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Stetter MG, Vidal-Villarejo M, Schmid KJ. Parallel Seed Color Adaptation during Multiple Domestication Attempts of an Ancient New World Grain. Mol Biol Evol 2019; 37:1407-1419. [DOI: 10.1093/molbev/msz304] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AbstractThousands of plants have been selected as crops; yet, only a few are fully domesticated. The lack of adaptation to agroecological environments of many crop plants with few characteristic domestication traits potentially has genetic causes. Here, we investigate the incomplete domestication of an ancient grain from the Americas, amaranth. Although three grain amaranth species have been cultivated as crop for millennia, all three lack key domestication traits. We sequenced 121 crop and wild individuals to investigate the genomic signature of repeated incomplete adaptation. Our analysis shows that grain amaranth has been domesticated three times from a single wild ancestor. One trait that has been selected during domestication in all three grain species is the seed color, which changed from dark seeds to white seeds. We were able to map the genetic control of the seed color adaptation to two genomic regions on chromosomes 3 and 9, employing three independent mapping populations. Within the locus on chromosome 9, we identify an MYB-like transcription factor gene, a known regulator for seed color variation in other plant species. We identify a soft selective sweep in this genomic region in one of the crop species but not in the other two species. The demographic analysis of wild and domesticated amaranths revealed a population bottleneck predating the domestication of grain amaranth. Our results indicate that a reduced level of ancestral genetic variation did not prevent the selection of traits with a simple genetic architecture but may have limited the adaptation of complex domestication traits.
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Affiliation(s)
- Markus G Stetter
- Botanical Institute, University of Cologne, Cologne, Germany
- Department of Plant Breeding, Population Genetics and Seed Science, University of Hohenheim, Stuttgart, Germany
| | - Mireia Vidal-Villarejo
- Department of Plant Breeding, Population Genetics and Seed Science, University of Hohenheim, Stuttgart, Germany
| | - Karl J Schmid
- Department of Plant Breeding, Population Genetics and Seed Science, University of Hohenheim, Stuttgart, Germany
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29
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Scott MF, Botigué LR, Brace S, Stevens CJ, Mullin VE, Stevenson A, Thomas MG, Fuller DQ, Mott R. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. NATURE PLANTS 2019; 5:1120-1128. [PMID: 31685951 PMCID: PMC6858886 DOI: 10.1038/s41477-019-0534-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/22/2019] [Indexed: 05/05/2023]
Abstract
Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.
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Affiliation(s)
- Michael F Scott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Laura R Botigué
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris J Stevens
- Institute of Archaeology, University College London, London, UK
| | | | - Alice Stevenson
- Institute of Archaeology, University College London, London, UK
| | - Mark G Thomas
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Dorian Q Fuller
- Institute of Archaeology, University College London, London, UK
| | - Richard Mott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
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30
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Wegary D, Teklewold A, Prasanna BM, Ertiro BT, Alachiotis N, Negera D, Awas G, Abakemal D, Ogugo V, Gowda M, Semagn K. Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands. Sci Rep 2019; 9:13490. [PMID: 31530852 PMCID: PMC6748982 DOI: 10.1038/s41598-019-49861-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/28/2019] [Indexed: 11/08/2022] Open
Abstract
Little is known on maize germplasm adapted to the African highland agro-ecologies. In this study, we analyzed high-density genotyping by sequencing (GBS) data of 298 African highland adapted maize inbred lines to (i) assess the extent of genetic purity, genetic relatedness, and population structure, and (ii) identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to highland environments. Nearly 91% of the pairs of inbred lines differed by 30-36% of the scored alleles, but only 32% of the pairs of the inbred lines had relative kinship coefficient <0.050, which suggests the presence of substantial redundancy in allelic composition that may be due to repeated use of fewer genetic backgrounds (source germplasm) during line development. Results from different genetic relatedness and population structure analyses revealed three different groups, which generally agrees with pedigree information and breeding history, but less so by heterotic groups and endosperm modification. We identified 944 single nucleotide polymorphic (SNP) markers that fell within 22 selective sweeps that harbored 265 protein-coding candidate genes of which some of the candidate genes had known functions. Details of the candidate genes with known functions and differences in nucleotide diversity among groups predicted based on multivariate methods have been discussed.
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Affiliation(s)
- Dagne Wegary
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Adefris Teklewold
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia.
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya
| | - Berhanu T Ertiro
- Bako National Maize Research Center, Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa, Ethiopia
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Demewez Negera
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Geremew Awas
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Demissew Abakemal
- Ambo Agricultural Research Center, P.O. Box 37, West Shoa, Ambo, Ethiopia
| | - Veronica Ogugo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya
| | - Kassa Semagn
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya.
- Africa Rice Center (AfricaRice), M'bé Research Station, 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
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31
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Zhang C, Zhu J, Chen S, Fan X, Li Q, Lu Y, Wang M, Yu H, Yi C, Tang S, Gu M, Liu Q. Wx lv, the Ancestral Allele of Rice Waxy Gene. MOLECULAR PLANT 2019; 12:1157-1166. [PMID: 31181338 DOI: 10.1016/j.molp.2019.05.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/30/2019] [Accepted: 05/28/2019] [Indexed: 05/07/2023]
Abstract
In rice grains, the Waxy (Wx) gene is responsible for the synthesis of amylose, the most important determinant for eating and cooking quality. The effects of several Wx alleles on amylose content and the taste of cooked rice have been elucidated. However, the relationship between artificial selection and the evolution of various Wx alleles as well as their distribution remain unclear. Here we report the identification of an ancestral allele, Wxlv, which dramatically affects the mouthfeel of rice grains by modulating the size of amylose molecules. We demonstrated that Wxlv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wxb, Wxa, and Wxin) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wxlv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.
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Affiliation(s)
- Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Jihui Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Shengjie Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiaolei Fan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Yan Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Min Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Chuandeng Yi
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Shuzhu Tang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China.
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Abstract
Rice is a staple crop for half the world's population, which is expected to grow by 3 billion over the next 30 years. It is also a key model for studying the genomics of agroecosystems. This dual role places rice at the centre of an enormous challenge facing agriculture: how to leverage genomics to produce enough food to feed an expanding global population. Scientists worldwide are investigating the genetic variation among domesticated rice species and their wild relatives with the aim of identifying loci that can be exploited to breed a new generation of sustainable crops known as Green Super Rice.
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Anacleto R, Badoni S, Parween S, Butardo VM, Misra G, Cuevas RP, Kuhlmann M, Trinidad TP, Mallillin AC, Acuin C, Bird AR, Morell MK, Sreenivasulu N. Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1261-1275. [PMID: 30549178 PMCID: PMC6575982 DOI: 10.1111/pbi.13051] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 11/15/2018] [Accepted: 11/25/2018] [Indexed: 05/19/2023]
Abstract
Reliably generating rice varieties with low glycaemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa ) explained the intermediate-to-high GI variation. A SNP (C˃T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non-starch polysaccharide pathway in lowering GI.
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Affiliation(s)
| | - Saurabh Badoni
- International Rice Research InstituteLos BañosPhilippines
| | - Sabiha Parween
- International Rice Research InstituteLos BañosPhilippines
| | - Vito M. Butardo
- International Rice Research InstituteLos BañosPhilippines
- Department of Chemistry and BiotechnologyFaculty of Science, Engineering and TechnologySwinburne University of TechnologyHawthornVic.Australia
| | - Gopal Misra
- International Rice Research InstituteLos BañosPhilippines
| | | | - Markus Kuhlmann
- The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | | | | | - Cecilia Acuin
- International Rice Research InstituteLos BañosPhilippines
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34
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Steensels J, Gallone B, Voordeckers K, Verstrepen KJ. Domestication of Industrial Microbes. Curr Biol 2019; 29:R381-R393. [DOI: 10.1016/j.cub.2019.04.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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35
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Faye JM, Maina F, Hu Z, Fonceka D, Cisse N, Morris GP. Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal. Ecol Evol 2019; 9:6038-6051. [PMID: 31161017 PMCID: PMC6540697 DOI: 10.1002/ece3.5187] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/22/2019] [Accepted: 03/29/2019] [Indexed: 02/01/2023] Open
Abstract
Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single-nucleotide polymorphisms (SNPs) using genotyping-by-sequencing. Seven subpopulations distributed along the north-south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay-green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome-wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate-associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.
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Affiliation(s)
- Jacques M. Faye
- Department of AgronomyKansas State UniversityManhattanKansas
| | - Fanna Maina
- Department of AgronomyKansas State UniversityManhattanKansas
- Institut National de la Recherche Agronomique du NigerNiameyNiger
| | - Zhenbin Hu
- Department of AgronomyKansas State UniversityManhattanKansas
| | - Daniel Fonceka
- Centre d'Étude Régional pour l'Amélioration de l'Adaptation à la SécheresseThièsSénégal
- CIRADUMR AGAPMontpellierFrance
| | - Ndiaga Cisse
- Centre d'Étude Régional pour l'Amélioration de l'Adaptation à la SécheresseThièsSénégal
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36
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Ndjiondjop MN, Alachiotis N, Pavlidis P, Goungoulou A, Kpeki SB, Zhao D, Semagn K. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1145-1158. [PMID: 30578434 PMCID: PMC6449321 DOI: 10.1007/s00122-018-3268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
Abstract
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Alphonse Goungoulou
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Sèdjro Bienvenu Kpeki
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Dule Zhao
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Kassa Semagn
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
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37
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Hardy CM, Burke MK, Everett LJ, Han MV, Lantz KM, Gibbs AG. Genome-Wide Analysis of Starvation-Selected Drosophila melanogaster-A Genetic Model of Obesity. Mol Biol Evol 2019; 35:50-65. [PMID: 29309688 DOI: 10.1093/molbev/msx254] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Experimental evolution affords the opportunity to investigate adaptation to stressful environments. Studies combining experimental evolution with whole-genome resequencing have provided insight into the dynamics of adaptation and a new tool to uncover genes associated with polygenic traits. Here, we selected for starvation resistance in populations of Drosophila melanogaster for over 80 generations. In response, the starvation-selected lines developed an obese condition, storing nearly twice the level of total lipids than their unselected controls. Although these fats provide a ∼3-fold increase in starvation resistance, the imbalance in lipid homeostasis incurs evolutionary cost. Some of these tradeoffs resemble obesity-associated pathologies in mammals including metabolic depression, low activity levels, dilated cardiomyopathy, and disrupted sleeping patterns. To determine the genetic basis of these traits, we resequenced genomic DNA from the selected lines and their controls. We found 1,046,373 polymorphic sites, many of which diverged between selection treatments. In addition, we found a wide range of genetic heterogeneity between the replicates of the selected lines, suggesting multiple mechanisms of adaptation. Genome-wide heterozygosity was low in the selected populations, with many large blocks of SNPs nearing fixation. We found candidate loci under selection by using an algorithm to control for the effects of genetic drift. These loci were mapped to a set of 382 genes, which associated with many processes including nutrient response, catabolic metabolism, and lipid droplet function. The results of our study speak to the evolutionary origins of obesity and provide new targets to understand the polygenic nature of obesity in a unique model system.
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Affiliation(s)
- Christopher M Hardy
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, OR
| | - Logan J Everett
- Department of Biological Sciences, North Carolina State University, Raleigh, NC
| | - Mira V Han
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Kathryn M Lantz
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Allen G Gibbs
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
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38
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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: 460] [Impact Index Per Article: 76.7] [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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39
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Wang DR, Agosto-Pérez FJ, Chebotarov D, Shi Y, Marchini J, Fitzgerald M, McNally KL, Alexandrov N, McCouch SR. An imputation platform to enhance integration of rice genetic resources. Nat Commun 2018; 9:3519. [PMID: 30158584 PMCID: PMC6115364 DOI: 10.1038/s41467-018-05538-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/05/2018] [Indexed: 12/22/2022] Open
Abstract
As sequencing and genotyping technologies evolve, crop genetics researchers accumulate increasing numbers of genomic data sets from various genotyping platforms on different germplasm panels. Imputation is an effective approach to increase marker density of existing data sets toward the goal of integrating resources for downstream applications. While a number of imputation software packages are available, the limitations to utilization for the rice community include high computational demand and lack of a reference panel. To address these challenges, we develop the Rice Imputation Server, a publicly available web application leveraging genetic information from a globally diverse rice reference panel assembled here. This resource allows researchers to benefit from increased marker density without needing to perform imputation on their own machines. We demonstrate improvements that imputed data provide to rice genome-wide association (GWA) results of grain amylose content and show that the major functional nucleotide polymorphism is tagged only in the imputed data set.
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Affiliation(s)
- Diane R Wang
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853-1901, USA
- Department of Geography, University at Buffalo, Buffalo, NY, 14261, USA
| | - Francisco J Agosto-Pérez
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Dmytro Chebotarov
- International Rice Research Institute, DAPO Box 7777,, 1301, Metro Manila, Philippines
| | - Yuxin Shi
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853-1901, USA
| | | | - Melissa Fitzgerald
- School of Agriculture and Food Science, University of Queensland, 4072, QLD, Brisbane, Australia
| | - Kenneth L McNally
- International Rice Research Institute, DAPO Box 7777,, 1301, Metro Manila, Philippines
| | - Nickolai Alexandrov
- International Rice Research Institute, DAPO Box 7777,, 1301, Metro Manila, Philippines
- Inari Agriculture Inc., Cambridge, Cambridge, MA, 02139, USA
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853-1901, USA.
- Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853-1901, USA.
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40
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Oh JH, Lee YJ, Byeon EJ, Kang BC, Kyeoung DS, Kim CK. Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants. 3 Biotech 2018; 8:115. [PMID: 29430376 PMCID: PMC5801106 DOI: 10.1007/s13205-018-1140-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/29/2018] [Indexed: 12/11/2022] Open
Abstract
Anthocyanins are involved in many diverse functions in rice, but their benefits have yet to be clearly demonstrated. Our objective in this study was to identify anthocyanin-related genes in black rice plants. We identified anthocyanin-related genes in black rice plants using a combination of whole-genome resequencing, RNA-sequencing (RNA-seq), microarray experiments, and reverse-transcriptase polymerase chain reaction (RT-PCR). Using multi-layer screening from 30 rice accessions, we identified 172,922 single-nucleotide polymorphisms (SNPs) and 1276 differentially expressed genes that appear to be related to anthocyanin biosynthesis. We identified 18 putative genes from 172,922 SNPs using intensive selective sweeps. The 18 candidate genes identified from SNPs were not significantly correlated with the RNA-seq expression pattern or other well-known anthocyanin biosynthesis/metabolism genes. We also identified nine putative genes from 1276 differentially expressed genes using RNA-seq transcriptome analysis. In addition, we identified four phylogenetic groups from these nine candidate genes and 51 pathway-network genes. Finally, we verified nine anthocyanin-related genes using a newly designed microarray and semi-quantitative RT-PCR. We suggest that these nine identified genes appear to be related to the regulation of anthocyanin biosynthesis and/or metabolism.
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Affiliation(s)
- Jae-Hyeon Oh
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874 Korea
| | - Ye-Ji Lee
- Department of Environmental Resources, Sangmyung University, Cheonan, 31066 Korea
| | - Eun-Ju Byeon
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju, 54896 Korea
| | - Byeong-Chul Kang
- Codes Division, Insilicogen Inc., Suwon, 16954 Gyeonggi-do Korea
| | - Dong-Soo Kyeoung
- Codes Division, Insilicogen Inc., Suwon, 16954 Gyeonggi-do Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874 Korea
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41
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Lundström M, Leino MW, Hagenblad J. Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat. BMC Genet 2017; 18:118. [PMID: 29262777 PMCID: PMC5738170 DOI: 10.1186/s12863-017-0566-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/09/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. In this study we trace the evolutionary history of the NAM-B1 in tetraploid wheat species and evaluate it as a putative domestication gene. RESULTS Genotyping of wild and landrace tetraploid accessions showed presence of only null alleles in durum. Domesticated emmer wheats contained both null alleles and the wild-type allele while wild emmers, with one exception, only carried the wild-type allele. One of the null alleles consists of a deletion that covers several 100 kb. The other null-allele, a one-basepair frame-shift insertion, likely arose among wild emmer. This allele was the target of a selective sweep, extending over several 100 kb. CONCLUSIONS The NAM-B1 gene fulfils some criteria for being a domestication gene by encoding a trait of domestication relevance (seed size) and is here shown to have been under positive selection. The presence of both wild-type and null alleles in domesticated emmer does, however, suggest the gene to be a diversification gene in this species. Further studies of genotype-environment interactions are needed to find out under what conditions selection on different NAM-B1 alleles have been beneficial.
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Affiliation(s)
- Maria Lundström
- Linköping University, IFM Biology, SE-581 83, Linköping, Sweden
| | - Matti W Leino
- Linköping University, IFM Biology, SE-581 83, Linköping, Sweden.,Nordiska museet, Swedish Museum of Cultural History, Box 27820, SE-115 93, Stockholm, Sweden.,The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Jenny Hagenblad
- Linköping University, IFM Biology, SE-581 83, Linköping, Sweden.
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42
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta. Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2017; 10:21. [PMID: 28523639 PMCID: PMC5436998 DOI: 10.1186/s12284-017-0161-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/09/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B. P. Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200 Kepala Batas, Pulau Pinang Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Ma. Teressa Sta. Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
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43
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2017. [PMID: 28523639 DOI: 10.1186/s12284-017-0161-6©] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B P Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ma Teressa Sta Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.
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Mathan J, Bhattacharya J, Ranjan A. Enhancing crop yield by optimizing plant developmental features. Development 2017; 143:3283-94. [PMID: 27624833 DOI: 10.1242/dev.134072] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A number of plant features and traits, such as overall plant architecture, leaf structure and morphological features, vascular architecture and flowering time are important determinants of photosynthetic efficiency and hence the overall performance of crop plants. The optimization of such developmental traits thus has great potential to increase biomass and crop yield. Here, we provide a comprehensive review of these developmental traits in crop plants, summarizing their genetic regulation and highlighting the potential of manipulating these traits for crop improvement. We also briefly review the effects of domestication on the developmental features of crop plants. Finally, we discuss the potential of functional genomics-based approaches to optimize plant developmental traits to increase yield.
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Affiliation(s)
- Jyotirmaya Mathan
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Juhi Bhattacharya
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Aashish Ranjan
- National Institute of Plant Genome Research, New Delhi 110067, India
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45
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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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46
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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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47
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Moyers BT, Morrell PL, McKay JK. Genetic Costs of Domestication and Improvement. J Hered 2017; 109:103-116. [DOI: 10.1093/jhered/esx069] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Brook T Moyers
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN (Morrell)
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO
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Sauvage C, Rau A, Aichholz C, Chadoeuf J, Sarah G, Ruiz M, Santoni S, Causse M, David J, Glémin S. Domestication rewired gene expression and nucleotide diversity patterns in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:631-645. [PMID: 28488328 DOI: 10.1111/tpj.13592] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/24/2017] [Accepted: 04/28/2017] [Indexed: 05/25/2023]
Abstract
Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co-expressed DEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co-expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific to DEG. Our study provides an extensive profiling of the rewiring of gene co-expression induced by the domestication syndrome in one of the main crop species.
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Affiliation(s)
- Christopher Sauvage
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - 67 Allée des Chênes - CS 60094, 84143, Montfavet Cedex, France
| | - Andrea Rau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Charlotte Aichholz
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - 67 Allée des Chênes - CS 60094, 84143, Montfavet Cedex, France
| | - Joël Chadoeuf
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - 67 Allée des Chênes - CS 60094, 84143, Montfavet Cedex, France
| | - Gautier Sarah
- Montpellier SupAgro, UMR 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398, Montpellier, France
| | - Manuel Ruiz
- CIRAD, UMR AGAP, Baillarguet, F-34980, Montferrier-sur-Lez, France
| | - Sylvain Santoni
- Montpellier SupAgro, UMR 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398, Montpellier, France
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice - 67 Allée des Chênes - CS 60094, 84143, Montfavet Cedex, France
| | - Jacques David
- Montpellier SupAgro, UMR 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398, Montpellier, France
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution de Montpellier (ISEM-UMR 5554 Université de Montpellier - CNRS-IRD-EPHE), F-34095, Montpellier, France
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, 75236, Uppsala, Sweden
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Plekhanova E, Vishnyakova MA, Bulyntsev S, Chang PL, Carrasquilla-Garcia N, Negash K, Wettberg EV, Noujdina N, Cook DR, Samsonova MG, Nuzhdin SV. Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits. Sci Rep 2017; 7:4816. [PMID: 28684880 PMCID: PMC5500531 DOI: 10.1038/s41598-017-05087-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 05/24/2017] [Indexed: 12/30/2022] Open
Abstract
The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy.
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Affiliation(s)
- Elena Plekhanova
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Margarita A Vishnyakova
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - Sergey Bulyntsev
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - Peter L Chang
- Department of Plant Pathology, University of California, Davis, CA, USA.,Program Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Kassaye Negash
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Eric von Wettberg
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, USA
| | - Nina Noujdina
- School of Architecture, University of Southern California, Los Angeles, CA, USA
| | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Maria G Samsonova
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Sergey V Nuzhdin
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia. .,Program Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA.
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50
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Wei X, Jiao G, Lin H, Sheng Z, Shao G, Xie L, Tang S, Xu Q, Hu P. GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:134-153. [PMID: 27957808 DOI: 10.1111/jipb.12510] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/12/2016] [Indexed: 05/26/2023]
Abstract
Rice grain filling determines grain weight, final yield and grain quality. Here, a rice defective grain filling mutant, gif2, was identified. Grains of gif2 showed a slower filling rate and a significant lower final grain weight and yield compared to wild-type. The starch content in gif2 was noticeably decreased and its physicochemical properties were also altered. Moreover, gif2 endosperm cells showed obvious defects in compound granule formation. Positional cloning identified GIF2 to encode an ADP-glucose pyrophosphorylase (AGP) large subunit, AGPL2; consequently, AGP enzyme activity in gif2 endosperms was remarkably decreased. GIF2 is mainly expressed in developing grains and the coded protein localizes in the cytosol. Yeast two hybrid assay showed that GIF2 interacted with AGP small subunits OsAGPS1, OsAGPS2a and OsAGPS2b. Transcript levels for granule-bound starch synthase, starch synthase, starch branching enzyme and starch debranching enzyme were distinctly elevated in gif2 grains. In addition, the level of nucleotide diversity of the GIF2 locus was extremely low in both cultivated and wild rice. All of these results suggest that GIF2 plays important roles in the regulation of grain filling and starch biosynthesis during caryopsis development, and that it has been preserved during selection throughout domestication of modern rice.
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Affiliation(s)
- Xiangjin Wei
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Haiyan Lin
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Qingguo Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
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