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Tian H, Zhang H, Shi X, Ma W, Zhang J. Population genetic diversity and environmental adaptation of Tamarix hispida in the Tarim Basin, arid Northwestern China. Heredity (Edinb) 2024:10.1038/s41437-024-00714-0. [PMID: 39138378 DOI: 10.1038/s41437-024-00714-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/06/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Arid ecosystems, characterized by severe water scarcity, play a crucial role in preserving Earth's biodiversity and resources. The Tarim Basin in Northwestern China, a typical arid region isolated by the Tianshan Mountains and expansive deserts, provides a special study area for investigating how plant response and adaptation to such environments. Tamarix hispida, a species well adapted to saline-alkaline and drought conditions, dominates in the saline-alkali lands of the Tarim Basin. This study aims to examine the genetic diversity and environmental adaptation of T. hispida in the Tarim Basin. Genomic SNPs for a total of 160 individuals from 17 populations were generated using dd-RAD sequencing approach. Population genetic structure and genetic diversity were analyzed by methods including ADMIXTURE, PCA, and phylogenetic tree. Environmental association analysis (EAA) was performed using LFMM and RDA analyses. The results revealed two major genetic lineages with geographical substitution patterns from west to east, indicating significant gene flow and hybridization. Environmental factors such as Precipitation Seasonality (bio15) and Topsoil Sand Fraction (T_SAND) significantly shaped allele frequencies, supporting the species' genetic adaptability. Several genes associated with environmental adaptation were identified and annotated, highlighting physiological and metabolic processes crucial for survival in arid conditions. The study highlights the role of geographical isolation and environmental factors in shaping genetic structure and adaptive evolution. The identified adaptive genes related to stress tolerance emphasize the species' resilience and highlight the importance of specific physiological and metabolic pathways.
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Affiliation(s)
- Haowen Tian
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- Xinjiang Key Laboratory of Conservation and Utilization of Gene Resources, Urumqi, Xinjiang, China
- Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Hongxiang Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China.
- Xinjiang Key Laboratory of Conservation and Utilization of Gene Resources, Urumqi, Xinjiang, China.
- Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China.
| | - Xiaojun Shi
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
| | - Wenhui Ma
- College of Ecology and Environment, Xinjiang University, Urumqi, 830046, China
| | - Jian Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- Xinjiang Key Laboratory of Conservation and Utilization of Gene Resources, Urumqi, Xinjiang, China
- Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
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Huang C, Cheng Y, Hu Y, Zhang X, Chen J, Zhao T, Si Z, Cao Y, Li Y, Fang L, Guan X, Zhang T. Impacts of parental genomic divergence in non-syntenic regions on cotton heterosis. J Adv Res 2024:S2090-1232(24)00331-X. [PMID: 39111623 DOI: 10.1016/j.jare.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 08/04/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024] Open
Abstract
INTRODUCTION Heterosis has revolutionized crop breeding, enhancing global agricultural production. However, the mechanisms underlying heterosis remain obscure. Xiangzamian 2# (XZM2), a super hybrid upland cotton (Gossypium hirsutum L.) characterized by high-yield heterosis, has been developed and extensively planted in China. OBJECTIVES We conducted a systematic analysis of CRI12 and J8891, two parents of XZM2. We aimed to reveal the precise genetic information and the role of non-syntenic divergence in shaping heterosis, laying a foundation for advancing understanding of heterosis. METHODS We de novo assembled high-quality genomes of CRI12 and J8891, and further uncovered abundant genetic variations and non-syntenic regions between the parents. Whole-genome comparison, association analysis, transcriptomic analysis and relative identity-by-descent (rIBD) estimation were conducted to identify structural variations (SVs) and introgressions within non-syntenic blocks and to analyze their impacts on promoting heterosis. RESULTS Parental genetic divergence increased in non-syntenic regions. Furthermore, these regions, accounting for only 16.71% of the total genome, contained more loci with significantly higher heterotic effects, far exceeding the syntenic background. SVs covered 97.26% of non-syntenic sequences and caused widespread gene expression differences in these regions, driving dynamic complementation of gene expression in the hybrid. A set of SVs were responsible for trait improvement and had positive effects on heterosis, contributing larger heritability than short variations. We characterized numerous parental-specific introgressions from G. barbadense. Specifically, a functional introgression segment within non-syntenic blocks introduced an elite haplotype, which significantly increased lint yield and enhanced heterosis. CONCLUSION Our study clarified non-syntenic regions to harbor more loci with higher heterotic effects, revealed their importance in promoting heterosis and supported the crucial role of genetic complementation in heterosis. SVs and introgressions were identified as key factors responsible for non-syntenic divergence between the parents. They had important effects on gene expression and trait improvement, positively contributing to heterosis.
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Affiliation(s)
- Chujun Huang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yu Cheng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yiwen Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yiqian Li
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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Qi G, Si Z, Xuan L, Han Z, Hu Y, Fang L, Dai F, Zhang T. Unravelling the genetic basis and regulation networks related to fibre quality improvement using chromosome segment substitution lines in cotton. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39046162 DOI: 10.1111/pbi.14436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/02/2024] [Accepted: 07/06/2024] [Indexed: 07/25/2024]
Abstract
The elucidation of genetic architecture and molecular regulatory networks underlying complex traits remains a significant challenge in life science, largely due to the substantial background effects that arise from epistasis and gene-environment interactions. The chromosome segment substitution line (CSSL) is an ideal material for genetic and molecular dissection of complex traits due to its near-isogenic properties; yet a comprehensive analysis, from the basic identification of substitution segments to advanced regulatory network, is still insufficient. Here, we developed two cotton CSSL populations on the Gossypium hirsutum background, representing wide adaptation and high lint yield, with introgression from G. barbadense, representing superior fibre quality. We sequenced 99 CSSLs that demonstrated significant differences from G. hirsutum in fibre, and characterized 836 dynamic fibre transcriptomes in three crucial developmental stages. We developed a workflow for precise resolution of chromosomal substitution segments; the genome sequencing revealed substitutions collectively representing 87.25% of the G. barbadense genome. Together, the genomic and transcriptomic survey identified 18 novel fibre-quality-related quantitative trait loci with high genetic contributions and the comprehensive landscape of fibre development regulation. Furthermore, analysis determined unique cis-expression patterns in CSSLs to be the driving force for fibre quality alteration; building upon this, the co-expression regulatory network revealed biological relationships among the noted pathways and accurately described the molecular interactions of GhHOX3, GhRDL1 and GhEXPA1 during fibre elongation, along with reliable predictions for their interactions with GhTBA8A5. Our study will enhance more strategic employment of CSSL in crop molecular biology and breeding programmes.
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Affiliation(s)
- Guoan Qi
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhanfeng Si
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lisha Xuan
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zegang Han
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Hu
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lei Fang
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fan Dai
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tianzhen Zhang
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
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Zheng HZ, Dai W, Xu MH, Lin YY, Zhu XL, Long H, Tong LL, Xu XG. Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses. Genes (Basel) 2024; 15:940. [PMID: 39062719 PMCID: PMC11275416 DOI: 10.3390/genes15070940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914-157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.
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Affiliation(s)
- Hao-Zhi Zheng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Wei Dai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Meng-Han Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Yu-Ye Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Xing-Li Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Hui Long
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
| | - Li-Li Tong
- School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing 210038, China;
| | - Xiao-Gang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (H.-Z.Z.); (W.D.); (M.-H.X.); (Y.-Y.L.); (X.-L.Z.); (H.L.)
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
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Cao S, Sawettalake N, Li P, Fan S, Shen L. DNA methylation variations underlie lettuce domestication and divergence. Genome Biol 2024; 25:158. [PMID: 38886807 PMCID: PMC11184767 DOI: 10.1186/s13059-024-03310-x] [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: 06/30/2023] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated from a single wild ancestor Lactuca serriola and subsequently diverged into two major morphologically distinct vegetable types: leafy lettuce and stem lettuce. However, the role of epigenetic variation in lettuce domestication and divergence remains largely unknown. RESULTS To understand the genetic and epigenetic basis underlying lettuce domestication and divergence, we generate single-base resolution DNA methylomes from 52 Lactuca accessions, including major lettuce cultivars and wild relatives. We find a significant increase of DNA methylation during lettuce domestication and uncover abundant epigenetic variations associated with lettuce domestication and divergence. Interestingly, DNA methylation variations specifically associated with leafy and stem lettuce are related to regulation and metabolic processes, respectively, while those associated with both types are enriched in stress responses. Moreover, we reveal that domestication-induced DNA methylation changes could influence expression levels of nearby and distal genes possibly through affecting chromatin accessibility and chromatin loop. CONCLUSION Our study provides population epigenomic insights into crop domestication and divergence and valuable resources for further domestication for diversity and epigenetic breeding to boost crop improvement.
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Affiliation(s)
- Shuai Cao
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Nunchanoke Sawettalake
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Ping Li
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Sheng Fan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
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Hu XZ, Guo C, Qin SY, Li DZ, Guo ZH. Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae). PLANT DIVERSITY 2024; 46:344-352. [PMID: 38798728 PMCID: PMC11119509 DOI: 10.1016/j.pld.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 05/29/2024]
Abstract
Pseudosasa gracilis (Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps. nanunica and Sinosasa polytricha reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of Ps. gracilis. Both plastid and nuclear data indicate that Ps. gracilis is more closely related to Sinosasa, which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 "perfect-copy" syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing Ps. gracilis was a hybrid descendant between Sinosasa longiligulata and Ps. nanunica, with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between Ps. gracilis and S. polytricha in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps. gracilis. By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.
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Affiliation(s)
- Xiang-Zhou Hu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Sheng-Yuan Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Su Y, Yu Z, Yang Y, Wong KC, Li X. Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307280. [PMID: 38380499 DOI: 10.1002/advs.202307280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Indexed: 02/22/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a robust method for studying gene expression at the single-cell level, but accurately quantifying genetic material is often hindered by limited mRNA capture, resulting in many missing expression values. Existing imputation methods rely on strict data assumptions, limiting their broader application, and lack reliable supervision, leading to biased signal recovery. To address these challenges, authors developed Bis, a distribution-agnostic deep learning model for accurately recovering missing sing-cell gene expression from multiple platforms. Bis is an optimal transport-based autoencoder model that can capture the intricate distribution of scRNA-seq data while addressing the characteristic sparsity by regularizing the cellular embedding space. Additionally, they propose a module using bulk RNA-seq data to guide reconstruction and ensure expression consistency. Experimental results show Bis outperforms other models across simulated and real datasets, showcasing superiority in various downstream analyses including batch effect removal, clustering, differential expression analysis, and trajectory inference. Moreover, Bis successfully restores gene expression levels in rare cell subsets in a tumor-matched peripheral blood dataset, revealing developmental characteristics of cytokine-induced natural killer cells within a head and neck squamous cell carcinoma microenvironment.
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Affiliation(s)
- Yanchi Su
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Zhuohan Yu
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
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Quiroz LF, Gondalia N, Brychkova G, McKeown PC, Spillane C. Haploid rhapsody: the molecular and cellular orchestra of in vivo haploid induction in plants. THE NEW PHYTOLOGIST 2024; 241:1936-1949. [PMID: 38180262 DOI: 10.1111/nph.19523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
In planta haploid induction (HI), which reduces the chromosome number in the progeny after fertilization, has garnered increasing attention for its significant potential in crop breeding and genetic research. Despite the identification of several natural and synthetic HI systems in different plant species, the molecular and cellular mechanisms underlying these HI systems remain largely unknown. This review synthesizes the current understanding of HI systems in plants (with a focus on genes and molecular mechanisms involved), including the molecular and cellular interactions which orchestrate the HI process. As most HI systems can function across taxonomic boundaries, we particularly discuss the evidence for conserved mechanisms underlying the process. These include mechanisms involved in preserving chromosomal integrity, centromere function, gamete communication and/or fusion, and maintenance of karyogamy. While significant discoveries and advances on haploid inducer systems have arisen over the past decades, we underscore gaps in understanding and deliberate on directions for further research for a more comprehensive understanding of in vivo HI processes in plants.
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Affiliation(s)
- Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Nikita Gondalia
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Galina Brychkova
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
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Liu X, Li P, Ding X, Wang Y, Qi G, Yu J, Zeng Y, Cai D, Yang X, Yang J, Xu C, Liu B, Dong Y, Zhao N. The Population Divergence and Genetic Basis of Local Adaptation of Wild Soybean ( Glycine soja) in China. PLANTS (BASEL, SWITZERLAND) 2023; 12:4128. [PMID: 38140455 PMCID: PMC10747053 DOI: 10.3390/plants12244128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/03/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023]
Abstract
Glycine soja is the wild relative species of cultivated soybean. In this study, we investigated the population divergence and genetic basis of the local adaptation of wild soybean in China using genome-wide single-nucleotide polymorphisms (SNPs) of a population of 72 G. soja accessions. Using phylogenetic analysis, we observed that G. soja accessions clustered into three distinct groups, each corresponding to a specific geographic region, the northeastern region (NER), central region (CR), and southern region (SR), consistent with previous studies. Notably, we found a significant positive correlation between genetic and geographic distances. Further population structure analysis revealed each group was associated with an ancestral population and a specific geographic area. By utilizing the genome sequencing data of accessions from 16 different locations, we inferred the population history of these wild soybean groups. Our results indicate that the three groups diverged ~25,000 years ago, coinciding with the time of the last glacial maximum. The effective population size of the SR group expanded first, and subsequently, the NER and CR groups expanded approximately 5000 and 2500 years ago, respectively. Moreover, 83, 104, and 101 significant associated loci (SALs) were identified using genome-wide association analysis for annual mean temperature, annual precipitation, and latitude, respectively. Functional analysis of genes located in SALs highlighted candidate genes related to local adaptation. This study highlights the significant role of geographic isolation and environmental factors in shaping the genetic structure and adaptability of wild soybean populations. Furthermore, it emphasizes the value of wild soybean as a crucial genetic resource for enhancing the adaptability of cultivated soybeans, which have experienced a loss of genetic diversity due to domestication and intensive breeding practices. The insights gained from our research provide valuable information for the protection, conservation, and utilization of this important genetic resource.
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Affiliation(s)
- Xiaodong Liu
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China; (X.L.)
- Jilin Academy of Agricultural Sciences, Changchun 130033, China (G.Q.); (J.Y.)
| | - Peiyuan Li
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China; (X.L.)
| | - Xiaoyang Ding
- Jilin Academy of Agricultural Sciences, Changchun 130033, China (G.Q.); (J.Y.)
| | - Ying Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.W.); (J.Y.); (Y.Z.); (B.L.)
| | - Guangxun Qi
- Jilin Academy of Agricultural Sciences, Changchun 130033, China (G.Q.); (J.Y.)
| | - Jiaxin Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.W.); (J.Y.); (Y.Z.); (B.L.)
| | - Yong Zeng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.W.); (J.Y.); (Y.Z.); (B.L.)
| | - Dezhi Cai
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China; (X.L.)
| | - Xuhang Yang
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China; (X.L.)
| | - Jiahui Yang
- Jilin Academy of Agricultural Sciences, Changchun 130033, China (G.Q.); (J.Y.)
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.W.); (J.Y.); (Y.Z.); (B.L.)
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.W.); (J.Y.); (Y.Z.); (B.L.)
| | - Yingshan Dong
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China; (X.L.)
- Jilin Academy of Agricultural Sciences, Changchun 130033, China (G.Q.); (J.Y.)
| | - Na Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China; (X.L.)
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10
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Liang R, Liu JL, Ji XQ, Olsen KM, Qiang S, Song XL. Fitness and Hard Seededness of F 2 and F 3 Descendants of Hybridization between Herbicide-Resistant Glycine max and G. soja. PLANTS (BASEL, SWITZERLAND) 2023; 12:3671. [PMID: 37960027 PMCID: PMC10650743 DOI: 10.3390/plants12213671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
The commercial cultivation of herbicide-resistant (HR) transgenic soybeans (Glycine max L. Merr.) raises great concern that transgenes may introgress into wild soybeans (Glycine soja Sieb. et Zucc.) via pollen-mediated gene flow, which could increase the ecological risks of transgenic weed populations and threaten the genetic diversity of wild soybean. To assess the fitness of hybrids derived from transgenic HR soybean and wild soybean, the F2 and F3 descendants of crosses of the HR soybean line T14R1251-70 and two wild soybeans (LNTL and JLBC, which were collected from LiaoNing TieLing and JiLin BaiCheng, respectively), were planted along with their parents in wasteland or farmland soil, with or without weed competition. The fitness of F2 and F3 was significantly increased compared to the wild soybeans under all test conditions, and they also showed a greater competitive ability against weeds. Seeds produced by F2 and F3 were superficially similar to wild soybeans in having a hard seed coat; however, closer morphological examination revealed that the hard-seededness was lower due to the seed coat structure, specifically the presence of thicker hourglass cells in seed coat layers and lower Ca content in palisade epidermis. Hybrid descendants containing the cp4-epsps HR allele were able to complete their life cycle and produce a large number of seeds in the test conditions, which suggests that they would be able to survive in the soil beyond a single growing season, germinate, and grow under suitable conditions. Our findings indicate that the hybrid descendants of HR soybean and wild soybean may pose potential ecological risks in regions of soybean cultivation where wild soybean occurs.
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Affiliation(s)
- Rong Liang
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
| | - Jia-Li Liu
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
| | - Xue-Qin Ji
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
| | - Kenneth M. Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA;
| | - Sheng Qiang
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
| | - Xiao-Ling Song
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
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11
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Hay NM, Windham MD, Mandáková T, Lysak MA, Hendriks KP, Mummenhoff K, Lens F, Pryer KM, Bailey CD. A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets. AMERICAN JOURNAL OF BOTANY 2023; 110:e16226. [PMID: 37561651 DOI: 10.1002/ajb2.16226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
PREMISE Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae. METHODS To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae-specific bait set designed for use in the mustard family. Relationships for 101 samples representing 81 currently recognized species were inferred from a total of 1114 low-copy nuclear genes using both supermatrix and species coalescence methods. RESULTS Our analyses resulted in a well-resolved and highly supported phylogeny of the tribe Boechereae. Boechereae is divided into two major clades, one comprising all western North American species of Boechera, the other encompassing the eight other genera of the tribe. Our understanding of relationships within Boechera is enhanced by the recognition of three core clades that are further subdivided into robust regional species complexes. CONCLUSIONS This study presents the first broadly sampled, well-resolved phylogeny for most known sexual diploid Boechera. This effort provides the foundation for a new phylogenetically informed taxonomy of Boechera that is crucial for its continued use as a model system.
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Affiliation(s)
- Nikolai M Hay
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Michael D Windham
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kasper P Hendriks
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
| | - Frederic Lens
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
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12
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Gao P, Zhao H, Luo Z, Lin Y, Feng W, Li Y, Kong F, Li X, Fang C, Wang X. SoyDNGP: a web-accessible deep learning framework for genomic prediction in soybean breeding. Brief Bioinform 2023; 24:bbad349. [PMID: 37824739 DOI: 10.1093/bib/bbad349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
Soybean is a globally significant crop, playing a vital role in human nutrition and agriculture. Its complex genetic structure and wide trait variation, however, pose challenges for breeders and researchers aiming to optimize its yield and quality. Addressing this biological complexity requires innovative and accurate tools for trait prediction. In response to this challenge, we have developed SoyDNGP, a deep learning-based model that offers significant advancements in the field of soybean trait prediction. Compared to existing methods, such as DeepGS and DNNGP, SoyDNGP boasts a distinct advantage due to its minimal increase in parameter volume and superior predictive accuracy. Through rigorous performance comparison, including prediction accuracy and model complexity, SoyDNGP represents improved performance to its counterparts. Furthermore, it effectively predicted complex traits with remarkable precision, demonstrating robust performance across different sample sizes and trait complexities. We also tested the versatility of SoyDNGP across multiple crop species, including cotton, maize, rice and tomato. Our results showed its consistent and comparable performance, emphasizing SoyDNGP's potential as a versatile tool for genomic prediction across a broad range of crops. To enhance its accessibility to users without extensive programming experience, we designed a user-friendly web server, available at http://xtlab.hzau.edu.cn/SoyDNGP. The server provides two features: 'Trait Lookup', offering users the ability to access pre-existing trait predictions for over 500 soybean accessions, and 'Trait Prediction', allowing for the upload of VCF files for trait estimation. By providing a high-performing, accessible tool for trait prediction, SoyDNGP opens up new possibilities in the quest for optimized soybean breeding.
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Affiliation(s)
- Pengfei Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Haonan Zhao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Zheng Luo
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Yifan Lin
- Hubei Hongshan Laboratory, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Wanjie Feng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Yaling Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Fanjiang Kong
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
| | - Chao Fang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xutong Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
- Hubei Hongshan Laboratory, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, China
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13
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Zhou X, Tian Y, Qu Z, Wang J, Han D, Dong S. Comparing the Salt Tolerance of Different Spring Soybean Varieties at the Germination Stage. PLANTS (BASEL, SWITZERLAND) 2023; 12:2789. [PMID: 37570942 PMCID: PMC10421394 DOI: 10.3390/plants12152789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
Salinization is a global agricultural problem with many negative effects on crops, including delaying germination, inhibiting growth, and reducing crop yield and quality. This study compared the salt tolerance of 20 soybean varieties at the germination stage to identify soybean germplasm with a high salt tolerance. Germination tests were conducted in Petri dishes containing 0, 50, 100, 150, and 200 mmol L-1 NaCl. Each Petri dish contained 20 soybean seeds, and each treatment was repeated five times. The indicators of germination potential, germination rate, hypocotyl length, and radicle length were measured. The salt tolerance of 20 soybean varieties was graded, and the theoretical identification concentration was determined by cluster analysis, the membership function method, one-way analysis of variance, and quadratic equation analysis. The relative germination rate, relative germination potential, relative root length, and relative bud length of the 20 soybean germplasms decreased when the salt concentration was >50 mmol L-1, compared with that of the Ctrl. The half-lethal salt concentration of soybean was 164.50 mmol L-1, and the coefficient of variation was 18.90%. Twenty soybean varieties were divided into three salt tolerance levels following cluster analysis: Dongnong 254, Heike 123, Heike 58, Heihe 49, and Heike 68 were salt-tolerant varieties, and Xihai 2, Suinong 94, Kenfeng 16, and Heinong 84 were salt-sensitive varieties, respectively. This study identified suitable soybean varieties for planting in areas severely affected by salt and provided materials for screening and extracting parents or genes to breed salt-tolerant varieties in areas where direct planting is impossible. It assists crop breeding at the molecular level to cope with increasingly serious salt stress.
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Affiliation(s)
- Xinyu Zhou
- Agricultural College, Northeast Agricultural University, Harbin 150030, China
| | - Yumei Tian
- Agricultural College, Northeast Agricultural University, Harbin 150030, China
| | - Zhipeng Qu
- Agricultural College, Northeast Agricultural University, Harbin 150030, China
| | - Jinxing Wang
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China
| | - Dezhi Han
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe 164399, China
| | - Shoukun Dong
- Agricultural College, Northeast Agricultural University, Harbin 150030, China
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14
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Li J, Lee CR. The role of gene presence-absence variations on genetic incompatibility in Asian rice. THE NEW PHYTOLOGIST 2023; 239:778-791. [PMID: 37194454 PMCID: PMC7615310 DOI: 10.1111/nph.18969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
Genetic incompatibilities are widespread between species. However, it remains unclear whether they all originated after population divergence as suggested by the Bateson-Dobzhansky-Muller model, and if not, what is their prevalence and distribution within populations. The gene presence-absence variations (PAVs) provide an opportunity for investigating gene-gene incompatibility. Here, we searched for the repulsion of coexistence between gene PAVs to identify the negative interaction of gene functions separately in two Oryza sativa subspecies. Many PAVs are involved in subspecies-specific negative epistasis and segregate at low-to-intermediate frequencies in focal subspecies but at low or high frequencies in the other subspecies. Incompatible PAVs are enriched in two functional groups, defense response and protein phosphorylation, which are associated with plant immunity and consistent with autoimmunity being a known mechanism of hybrid incompatibility in plants. Genes in the two enriched functional groups are older and seldom directly interact with each other. Instead, they interact with other younger gene PAVs with diverse functions. Our results illustrate the landscape of genetic incompatibility at gene PAVs in rice, where many incompatible pairs have already segregated as polymorphisms within subspecies, and many are novel negative interactions between older defense-related genes and younger genes with diverse functions.
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Affiliation(s)
- Juan Li
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 106319, Taiwan
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 106319, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei 106319, Taiwan
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15
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Jiao C, Hao C, Li T, Bohra A, Wang L, Hou J, Liu H, Liu H, Zhao J, Wang Y, Liu Y, Wang Z, Jing X, Wang X, Varshney RK, Fu J, Zhang X. Fast integration and accumulation of beneficial breeding alleles through an AB-NAMIC strategy in wheat. PLANT COMMUNICATIONS 2023; 4:100549. [PMID: 36642955 DOI: 10.1016/j.xplc.2023.100549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/26/2022] [Accepted: 01/11/2023] [Indexed: 05/11/2023]
Abstract
Wheat (Triticum aestivum) is among the most important staple crops for safeguarding the food security of the growing world population. To bridge the gap between genebank diversity and breeding programs, we developed an advanced backcross-nested association mapping plus inter-crossed population (AB-NAMIC) by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core collection. Selective backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB-NAMIC population. We performed phenotyping of 590 AB-NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP array. Genome-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in AB-NAMIC. Notably, genome-wide association studies in AB-NAMIC detected the candidate gene TaSWEET6-7B (TraesCS7B03G1216700), which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield traits. The commercial release of two derived AB-NAMIC lines attests to its direct applicability in wheat improvement. Valuable information on genome-wide association study mapping, candidate genes, and their haplotypes for breeding traits are available through WheatGAB. Our research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.
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Affiliation(s)
- Chengzhi Jiao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chenyang Hao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tian Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Abhishek Bohra
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Lanfen Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Hou
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongxia Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Zhao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yamei Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yunchuan Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiwei Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Jing
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia.
| | - Junjie Fu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xueyong Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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16
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Jia Y, Liu ML, López-Pujol J, Jia RW, Kou YX, Yue M, Guan TX, Li ZH. The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis. Mol Phylogenet Evol 2023; 182:107736. [PMID: 36805473 DOI: 10.1016/j.ympev.2023.107736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.
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Affiliation(s)
- Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona 08038, Catalonia, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Rui-Wen Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yi-Xuan Kou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Tian-Xia Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Key Laboratory of Hexi Corridor Resources Utilization of Gansu, College of Life Sciences and Engineering, Hexi University, Zhangye 734000, Gansu, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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17
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Wu YH, Hou SB, Yuan ZY, Jiang K, Huang RY, Wang K, Liu Q, Yu ZB, Zhao HP, Zhang BL, Chen JM, Wang LJ, Stuart BL, Chambers EA, Wang YF, Gao W, Zou DH, Yan F, Zhao GG, Fu ZX, Wang SN, Jiang M, Zhang L, Ren JL, Wu YY, Zhang LY, Yang DC, Jin JQ, Yin TT, Li JT, Zhao WG, Murphy RW, Huang S, Guo P, Zhang YP, Che J. DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs. Mol Ecol Resour 2023. [PMID: 36924341 DOI: 10.1111/1755-0998.13784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.
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Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shao-Bing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ru-Yi Huang
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Zhong-Bin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hai-Peng Zhao
- School of Life Science, Henan University, Kaifeng, Henan, 475001, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Li-Jun Wang
- School of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601, USA
| | - E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720, USA
| | - Yu-Fan Wang
- Zhejiang Forest Resource Monitoring Center, Hangzhou, Zhejiang, 310020, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Da-Hu Zou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Gui-Gang Zhao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Zhong-Xiong Fu
- Yunnan Senye Biotechnology Co., Ltd, Xishuangbanna, Yunnan, 666100, China
| | - Shao-Neng Wang
- Bureau of Guangxi Mao'er Mountain Nature Reserve, Guilin, Guangxi, 541316, China
| | - Ming Jiang
- Gongshan Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan, 650224, China
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Ya-Yong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Lu-Yang Zhang
- Beijing Mountains & Seas Eco Technology Co. Ltd, Beijing, 101100, China
| | - Dian-Cheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Wen-Ge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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18
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Rajpal VR, Singh A, Kathpalia R, Thakur RK, Khan MK, Pandey A, Hamurcu M, Raina SN. The Prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation. FRONTIERS IN PLANT SCIENCE 2023; 14:1127239. [PMID: 36998696 PMCID: PMC10044020 DOI: 10.3389/fpls.2023.1127239] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/22/2023] [Indexed: 05/31/2023]
Abstract
Crop wild relatives (CWRs), landraces and exotic germplasm are important sources of genetic variability, alien alleles, and useful crop traits that can help mitigate a plethora of abiotic and biotic stresses and crop yield reduction arising due to global climatic changes. In the pulse crop genus Lens, the cultivated varieties have a narrow genetic base due to recurrent selections, genetic bottleneck and linkage drag. The collection and characterization of wild Lens germplasm resources have offered new avenues for the genetic improvement and development of stress-tolerant, climate-resilient lentil varieties with sustainable yield gains to meet future food and nutritional requirements. Most of the lentil breeding traits such as high-yield, adaptation to abiotic stresses and resistance to diseases are quantitative and require the identification of quantitative trait loci (QTLs) for marker assisted selection and breeding. Advances in genetic diversity studies, genome mapping and advanced high-throughput sequencing technologies have helped identify many stress-responsive adaptive genes, quantitative trait loci (QTLs) and other useful crop traits in the CWRs. The recent integration of genomics technologies with plant breeding has resulted in the generation of dense genomic linkage maps, massive global genotyping, large transcriptomic datasets, single nucleotide polymorphisms (SNPs), expressed sequence tags (ESTs) that have advanced lentil genomic research substantially and allowed for the identification of QTLs for marker-assisted selection (MAS) and breeding. Assembly of lentil and its wild species genomes (~4Gbp) opens up newer possibilities for understanding genomic architecture and evolution of this important legume crop. This review highlights the recent strides in the characterization of wild genetic resources for useful alleles, development of high-density genetic maps, high-resolution QTL mapping, genome-wide studies, MAS, genomic selections, new databases and genome assemblies in traditionally bred genus Lens for future crop improvement amidst the impending global climate change.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
| | - Renu Kathpalia
- Department of Botany, Kirori Mal College, University of Delhi, Delhi, India
| | - Rakesh Kr. Thakur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
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19
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Vega M, Quintero-Corrales C, Mastretta-Yanes A, Casas A, López-Hilario V, Wegier A. Multiple domestication events explain the origin of Gossypium hirsutum landraces in Mexico. Ecol Evol 2023; 13:e9838. [PMID: 36911302 PMCID: PMC9994486 DOI: 10.1002/ece3.9838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 03/14/2023] Open
Abstract
Several Mesoamerican crops constitute wild-to-domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene-introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene-introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI-wild, landraces, TI-landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation.
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Affiliation(s)
- Melania Vega
- Genética de la Conservación, Jardín Botánico Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de México Mexico.,Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Christian Quintero-Corrales
- Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México Ciudad de México Mexico.,Departamento de Botánica Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO) Ciudad de México Mexico.,Consejo Nacional de Ciencia y Tecnología (CONACYT) Programa de Investigadores e Investigadoras por México Ciudad de México Mexico
| | - Alejandro Casas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad Universidad Nacional Autónoma de México Morelia Mexico
| | | | - Ana Wegier
- Genética de la Conservación, Jardín Botánico Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de México Mexico
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20
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Imran M, Shafiq S, Tang X. CRISPR-Cas9-mediated editing of BADH2 gene triggered fragrance revolution in rice. PHYSIOLOGIA PLANTARUM 2023; 175:e13871. [PMID: 36748269 DOI: 10.1111/ppl.13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 12/26/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Fragrance is one of the most important quality traits for breeding in rice. The natural aroma substance 2-acetyl-1-pyrroline (2-AP) is a key fragrance compound among over 200 volatiles identified in fragrant rice. In addition to rice, there are other plant species that contain a germplasm that naturally produces a fragrant aroma. These other plant species all have lower activity levels of the enzyme BETAINE ALDEHYDE DEHYDROGENASE 2 (BADH2). Therefore, improving fragrance efficiency has been a focus of intensive research. Recent studies have engineered BADH2 gene, which is responsible for fragrance trait in non-fragrant cultivars of rice, using CRISPR-Cas9. Although engineering rice BADH2 can be useful for upregulating 2-AP, there are still a lot of restrictions on how it can be applied in practice. In this review article, we discuss the recent developments in BADH2 editing and propose potential future strategies to effectively target BADH2 for transcriptional regulation, with the goal of producing a better fragrance.
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Affiliation(s)
- Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
- Yingdong College of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Ontario, Canada
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
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21
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Nan J, Ling Y, An J, Wang T, Chai M, Fu J, Wang G, Yang C, Yang Y, Han B. Genome resequencing reveals independent domestication and breeding improvement of naked oat. Gigascience 2022; 12:giad061. [PMID: 37524540 PMCID: PMC10390318 DOI: 10.1093/gigascience/giad061] [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: 11/09/2022] [Revised: 05/04/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
As an important cereal crop, common oat, has attracted more and more attention due to its healthy nutritional components and bioactive compounds. Here, high-depth resequencing of 115 oat accessions and closely related hexaploid species worldwide was performed. Based on genetic diversity and linkage disequilibrium analysis, it was found that hulled oat (Avena sativa) experienced a more severe bottleneck than naked oat (Avena sativa var. nuda). Combined with the divergence time of ∼51,200 years ago, the previous speculation that naked oat was a variant of hulled oat was rejected. It was found that the common segments that hulled oat introgressed to naked oat cultivars contained 444 genes, mainly enriched in photosynthetic efficiency-related pathways. Selective sweeps during environmental adaptation and breeding improvement were identified in the naked oat genome. Candidate genes associated with smut resistance and the days to maturity phenotype were also identified. Our study provides genomic resources and new insights into naked oat domestication and breeding.
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Affiliation(s)
- Jinsheng Nan
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Yu Ling
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Jianghong An
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Ting Wang
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Mingna Chai
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Jun Fu
- Beijing 8omics Gene Technology Co. Ltd, Beijing 100080, China
| | - Gaochao Wang
- Beijing 8omics Gene Technology Co. Ltd, Beijing 100080, China
| | - Cai Yang
- Inner Mongolia Guomai Agriculture Co. Ltd, Xilingol League, Xilinhot City 026005, China
| | - Yan Yang
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Bing Han
- Key Laboratory of Germplasm Innovation and Utilization of Triticeae Crops at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot 010010, China
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22
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Han B, Zhang MJ, Xian Y, Xu H, Cui CC, Liu D, Wang L, Li DZ, Li WQ, Xie XM. Variations in genetic diversity in cultivated Pistacia chinensis. FRONTIERS IN PLANT SCIENCE 2022; 13:1030647. [PMID: 36438104 PMCID: PMC9691265 DOI: 10.3389/fpls.2022.1030647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39 P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.
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Affiliation(s)
- Biao Han
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Ming-Jia Zhang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yang Xian
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Hui Xu
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Cheng-Cheng Cui
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Dan Liu
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Lei Wang
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wen-Qing Li
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
| | - Xiao-Man Xie
- Key Laboratory of State Forestry and Grassland Administration Conservation and Utilization of Warm Temperate Zone Forest and Grass Germplasm Resources, Shandong Provincial Center of Forest and Grass Germplasm Resources, Ji’nan, Shandong, China
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23
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MacTavish R, Anderson JT. Water and nutrient availability exert selection on reproductive phenology. AMERICAN JOURNAL OF BOTANY 2022; 109:1702-1716. [PMID: 36031862 DOI: 10.1002/ajb2.16057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Global change has changed resource availability to plants, which could shift the adaptive landscape. We hypothesize that novel water and nutrient availability combinations alter patterns of natural selection on reproductive phenology in Boechera stricta (Brassicaceae) and influence the evolution of local adaptation. METHODS We conducted a multifactorial greenhouse study using 35 accessions of B. stricta sourced from a broad elevational gradient in the Rocky Mountains. We exposed full siblings to three soil water and two nutrient availability treatment levels, reflecting current and projected future conditions. In addition, we quantified fitness (seed count) and four phenological traits: the timing of first flowering, the duration of flowering, and height and leaf number at flowering. RESULTS Selection favored early flowering and longer duration of flowering, and the genetic correlation between these traits accorded with the direction of selection. In most treatments, we found selection for increased height, but selection on leaf number depended on water availability, with selection favoring more leaves in well-watered conditions and fewer leaves under severe drought. Low-elevation genotypes had the greatest fitness under drought stress, consistent with local adaptation. CONCLUSIONS We found evidence of strong selection on these heritable traits. Furthermore, the direction and strength of selection on size at flowering depended on the variable measured (height vs. leaf number). Finally, selection often favored both early flowering and a longer duration of flowering. Selection on these two components of phenology can be difficult to disentangle due to tight genetic correlations.
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Affiliation(s)
- Rachel MacTavish
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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24
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Arnqvist G, Sayadi A. A possible genomic footprint of polygenic adaptation on population divergence in seed beetles? Ecol Evol 2022; 12:e9440. [PMID: 36311399 PMCID: PMC9608792 DOI: 10.1002/ece3.9440] [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: 01/25/2022] [Revised: 09/14/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome‐wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate‐dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean FST = 0.23–0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's DNS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (dXY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome‐wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden
| | - Ahmed Sayadi
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden,Rheumatology, Department of Medical SciencesUppsala UniversityUppsalaSweden
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Song B, Li X, Cao B, Zhang M, Korban SS, Yu L, Yang W, Zhao K, Li J, Wu J. An identical-by-descent segment harbors a 12-bp insertion determining fruit softening during domestication and speciation in Pyrus. BMC Biol 2022; 20:215. [PMID: 36183077 PMCID: PMC9526952 DOI: 10.1186/s12915-022-01409-w] [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: 06/09/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the wild relatives of pear originated in southwest China, this fruit crop was independently domesticated and improved in Asia and Europe, and there are major phenotypic differences (e.g., maturity and fruit firmness) between Asian and European pears. RESULTS: In this study, we examined the genomes of 113 diverse pear accessions using an identity-by-descent (IBD) approach to investigate how historical gene flow has shaped fruit firmness traits in Asian and European pears. We found a 3-Mbp IBD-enriched region (IBD-ER) that has undergone "convergent domestication" in both the Asian and European pear lineages, and a genome-wide association study (GWAS) of fruit firmness phenotypes strongly implicated the TRANSLOCON AT THE INNER CHLOROPLAST ENVELOPE55 (TIC55) locus within this 3-Mbp IBD-ER. Furthermore, we identified a tandem duplication that includes a 12-bp insertion located in the first exon of TIC55 that is uniquely present in Asian pears, and expression analysis showed that the pear TIC55 gene is highly expressed in Asian pear, while it is weakly or not expressed in European pear; this could contribute to the differences in fruit firmness between Asian and European pear fruits. CONCLUSIONS Our findings provide insights into how pear fruit softening has been impacted during domestication, and we identified candidate genes associated with fruit softening that can contribute to the breeding and improvement of pear and other fruit crops.
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Affiliation(s)
- Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaolong Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Present Address: Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Beibei Cao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingyue Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Schuyler S Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Li'ang Yu
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14850, USA
| | - Wenxi Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Yang G, Deng P, Guo Q, Shi T, Pan W, Cui L, Liu X, Nie X. Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:450. [PMID: 36127641 PMCID: PMC9490906 DOI: 10.1186/s12870-022-03828-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are emerging as the important regulators involving in growth and development as well as stress response in plants. However, current lncRNA studies were mainly performed at the individual level and the significance of it is not well understood in wheat. RESULTS In this study, the lncRNA landscape of wheat spike was characterized through analysing a total of 186 spike RNA-seq datasets from 93 wheat genotypes. A total of 35,913 lncRNAs as well as 1,619 lncRNA-mRNA pairs comprised of 443 lncRNAs and 464 mRNAs were obtained. Compared to coding genes, these lncRNAs displayed rather low conservation among wheat and other gramineous species. Based on re-sequencing data, the genetic variations of these lncRNA were investigated and obvious genetic bottleneck were found on them during wheat domestication process. Furthermore, 122 lncRNAs were found to act as ceRNA to regulate endogenous competition. Finally, association and co-localization analysis of the candidate lncRNA-mRNA pairs identified 170 lncRNAs and 167 target mRNAs significantly associated with spike-related traits, including lncRNA.127690.1/TraesCS2A02G518500.1 (PMEI) and lncRNA.104854.1/TraesCS6A02G050300.1 (ATG5) associated with heading date and spike length, respectively. CONCLUSIONS This study reported the lncRNA landscape of wheat spike through the population transcriptome analysis, which not only contribute to better understand the wheat evolution from the perspective of lncRNA, but also lay the foundation for revealing roles of lncRNA playing in spike development.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qifan Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tingrui Shi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Xiaoqin Liu
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, Shandong, China.
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Zhou J, Yang Y, Lv Y, Pu Q, Li J, Zhang Y, Deng X, Wang M, Wang J, Tao D. Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L. FRONTIERS IN PLANT SCIENCE 2022; 13:932737. [PMID: 35845644 PMCID: PMC9280345 DOI: 10.3389/fpls.2022.932737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a comprehensive view of its original domestication, divergences, and the origin of different subgroups by integrating agriculture, archeology, genetics, nuclear, and cytoplasm genome results. Then, it was highlighted that interspecific hybridization-introgression has played important role in improving the genetic diversity and adaptation of Oryza sativa during its evolution process. Natural hybridization-introgression led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. We proposed a series to exploit the virtues of hybridization-introgression in the genetic improvement of Asian cultivated rice. But some key issues such as reproductive barriers especially hybrid sterility should be investigated further, which are conducive to gene exchange between cultivated rice and its relatives, and even is beneficial to exploiting interspecific hybrid vigor. New technologies help introduce favorable genes from distant wild species to Asian cultivated rice, such as transgenic and genome editing systems. Rising introgression lines in a wider range with multi-donor benefits allele mining, understanding genetic network of rice growth and development, yield formation, and environmental adaptation. Then, integration of new tools and interspecific hybridization can be a future direction to develop more usable breeding populations which can make Asian cultivated rice more resilient to the changing climate and world.
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Affiliation(s)
- Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ying Yang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yonggang Lv
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qiuhong Pu
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jing Li
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yu Zhang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xianneng Deng
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Min Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Jie Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Clark CB, Wang W, Wang Y, Fear GJ, Wen Z, Wang D, Ren B, Ma J. Identification and molecular mapping of a major quantitative trait locus underlying branch angle in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:777-784. [PMID: 34779894 DOI: 10.1007/s00122-021-03995-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/06/2021] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE A major quantitative trait locus (QTL) modulating soybean (Glycine max) branch angle was identified by linkage analysis using two bi-parental mapping populations with and without pedigree from wild soybean (Glycine soja). Soybean branch angle is a critical architectural trait that affects many other traits of agronomic importance associated with the plant's productivity and grain yield and is thus a vital consideration in soybean breeding. However, the genetic basis for modulating this important trait in soybean and many other crops remain unknown. Previously, we developed a recombinant inbred line (RIL) population derived from a cross between a domesticated soybean (Glycine max) variety, Williams 82, and a wild soybean (Glycine soja) accession, PI 479,752, and observed drastic variation in plant architecture including branch angle among individual RILs. In this study, one of the RILs possessing extremely wide branch angle (WBA) was crossed with an elite soybean cultivar (LD00-3309) possessing narrow branch angle (NBA) to produce an F2 population composed of 147 plants and F2-derived F3 families for inheritance analysis and QTL mapping. We found that branch angle is controlled by a major QTL located on chromosome 19, designated qGmBa1 and that WBA-derived from the wild soybean accession-is dominant over NBA. This locus was also detected as a major one underlying branch angle by QTL mapping using a subset of the soybean nested association mapping (SoyNAM) population composed of 140 RILs, which were derived from a cross between a landrace, PI 437169B, possessing WBA and an elite variety, IA3023, possessing NBA. Molecular markers located in the QTL region defined by both mapping populations can be used for marker-assisted selection of branch angle in soybean breeding.
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Affiliation(s)
- Chancelor B Clark
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Weidong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Ying Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- College of Plant Science, Jilin University, Changchun, Jilin, 130062, China
| | - Gabriel J Fear
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
- Syngenta, Research Triangle Park, Durham, NC, 27709, USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Bo Ren
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
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Griffiths M, Delory BM, Jawahir V, Wong KM, Bagnall GC, Dowd TG, Nusinow DA, Miller AJ, Topp CN. Optimisation of root traits to provide enhanced ecosystem services in agricultural systems: A focus on cover crops. PLANT, CELL & ENVIRONMENT 2022; 45:751-770. [PMID: 34914117 PMCID: PMC9306666 DOI: 10.1111/pce.14247] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/05/2021] [Accepted: 12/01/2021] [Indexed: 05/26/2023]
Abstract
Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical and biotic properties of soil. However, cover crops, a group of plants that provide ecosystem services, can be utilised during fallow periods or used as an intercrop to restore soil health. The effectiveness of ecosystem services provided by cover crops varies widely as very little breeding has occurred in these species. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. In this study, we provide an overview of the range of belowground ecosystem services provided by cover crop roots: (1) soil structural remediation, (2) capture of soil resources and (3) maintenance of the rhizosphere and building of organic matter content. Based on the ecosystem services described, we outline current and promising phenotyping technologies and breeding strategies in cover crops that can enhance agricultural sustainability through improvement of root traits.
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Affiliation(s)
| | | | | | - Kong M. Wong
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | | | - Tyler G. Dowd
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | | | - Allison J. Miller
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
- Department of BiologySaint Louis UniversitySt. LouisMissouriUSA
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30
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Ge J, Wang J, Pang H, Li F, Lou D, Fan W, Liu Z, Li J, Li D, Nong B, Zhang Z, Wang Y, Huang J, Xing M, Nie Y, Xiao X, Zhang F, Wang W, Xu J, Kim SR, Kohli A, Ye G, Qiao W, Yang Q, Zheng X. Genome-wide selection and introgression of Chinese rice varieties during breeding. J Genet Genomics 2022; 49:492-501. [DOI: 10.1016/j.jgg.2022.02.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/15/2022]
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Panzeri D, Guidi Nissim W, Labra M, Grassi F. Revisiting the Domestication Process of African Vigna Species (Fabaceae): Background, Perspectives and Challenges. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040532. [PMID: 35214865 PMCID: PMC8879845 DOI: 10.3390/plants11040532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 05/14/2023]
Abstract
Legumes are one of the most economically important and biodiverse families in plants recognised as the basis to develop functional foods. Among these, the Vigna genus stands out as a good representative because of its relatively recent African origin as well as its outstanding potential. Africa is a great biodiversity centre in which a great number of species are spread, but only three of them, Vigna unguiculata, Vigna subterranea and Vigna vexillata, were successfully domesticated. This review aims at analysing and valorising these species by considering the perspective of human activity and what effects it exerts. For each species, we revised the origin history and gave a focus on where, when and how many times domestication occurred. We provided a brief summary of bioactive compounds naturally occurring in these species that are fundamental for human wellbeing. The great number of wild lineages is a key point to improve landraces since the domestication process caused a loss of gene diversity. Their genomes hide a precious gene pool yet mostly unexplored, and genes lost during human activity can be recovered from the wild lineages and reintroduced in cultivated forms through modern technologies. Finally, we describe how all this information is game-changing to the design of future crops by domesticating de novo.
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Affiliation(s)
- Davide Panzeri
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
- Correspondence: (D.P.); (F.G.)
| | - Werther Guidi Nissim
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Viale delle Idee 30, 50019 Sesto Fiorentino, Italy
| | - Massimo Labra
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
| | - Fabrizio Grassi
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
- Correspondence: (D.P.); (F.G.)
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32
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Foria S, Magris G, Jurman I, Schwope R, De Candido M, De Luca E, Ivanišević D, Morgante M, Di Gaspero G. Extent of wild-to-crop interspecific introgression in grapevine (Vitis vinifera) as a consequence of resistance breeding and implications for the crop species definition. HORTICULTURE RESEARCH 2022; 9:uhab010. [PMID: 35039824 PMCID: PMC8801725 DOI: 10.1093/hr/uhab010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 01/18/2022] [Accepted: 09/25/2021] [Indexed: 05/31/2023]
Abstract
Over the past two centuries, introgression through repeated backcrossing has introduced disease resistance from wild grape species into the domesticated lineage Vitis vinifera subsp. sativa. Introgression lines are being cultivated over increasing vineyard surface areas, as their wines now rival in quality those obtained from preexisting varieties. There is, however, a lot of debate about whether and how wine laws defining commercial product categories, which are based on the classification of V. vinifera and interspecific hybrid grapes, should be revised to accommodate novel varieties that do not fit either category. Here, we developed a method of multilocus genotype analysis using short-read resequencing to identify haplotypic blocks of wild ancestry in introgression lines and quantify the physical length of chromosome segments free-of-introgression or with monoallelic and biallelic introgression. We used this genomic data to characterize species, hybrids and introgression lines and show that newly released resistant varieties contain 76.5-94.8% of V. vinifera DNA. We found that varietal wine ratings are not always commensurate with the percentage of V. vinifera ancestry and linkage drag of wild alleles around known resistance genes persists over at least 7.1-11.5 Mb, slowing down the recovery of the recurrent parental genome. This method also allowed us to identify the donor species of known resistance haplotypes, define the ancestry of wild genetic background in introgression lines with complex pedigrees, validate the ancestry of the historic varieties Concord and Norton, and unravel sample curation errors in public databases.
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Affiliation(s)
- Serena Foria
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
- Dr. Schär R&D Centre, Padriciano 99, 34149 Trieste, Italy
| | - Gabriele Magris
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Irena Jurman
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
| | - Rachel Schwope
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Massimo De Candido
- VCR Research Center, Vivai Cooperativi Rauscedo, Via Ruggero Forti 4, 33095 San Giorgio della Richinvelda, Italy
| | - Elisa De Luca
- VCR Research Center, Vivai Cooperativi Rauscedo, Via Ruggero Forti 4, 33095 San Giorgio della Richinvelda, Italy
| | - Dragoslav Ivanišević
- Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21102 Novi Sad, Serbia
| | - Michele Morgante
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
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Liu H, Yu J, Yu X, Zhang D, Chang H, Li W, Song H, Cui Z, Wang P, Luo Y, Wang F, Wang D, Li Z, Huang Z, Fu A, Xu M. Structural variation of mitochondrial genomes sheds light on evolutionary history of soybeans. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1456-1472. [PMID: 34587339 DOI: 10.1111/tpj.15522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/27/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
The architecture and genetic diversity of mitogenome (mtDNA) are largely unknown in cultivated soybean (Glycine max), which is domesticated from the wild progenitor, Glycine soja, 5000 years ago. Here, we de novo assembled the mitogenome of the cultivar 'Williams 82' (Wm82_mtDNA) with Illumina PE300 deep sequencing data, and verified it with polymerase chain reaction (PCR) and Southern blot analyses. Wm82_mtDNA maps as two autonomous circular chromosomes (370 871-bp Chr-m1 and 62 661-bp Chr-m2). Its structure is extensively divergent from that of the mono-chromosomal mitogenome reported in the landrace 'Aiganhuang' (AGH_mtDNA). Synteny analysis showed that the structural variations (SVs) between two genomes are mainly attributed to ectopic and illegitimate recombination. Moreover, Wm82_mtDNA and AGH_mtDNA each possess six and four specific regions, which are absent in their counterparts and likely result from differential sequence-loss events. Mitogenome SV was further studied in 39 wild and 182 cultivated soybean accessions distributed world-widely with PCR/Southern analyses or a comparable in silico analysis. The results classified both wild and cultivated soybeans into five cytoplasmic groups, named as GSa-GSe and G1-G5; 'Williams 82' and 'Aiganhuang' belong to G1 and G5, respectively. Notably, except for members in GSe and G5, all accessions carry a bi-chromosomal mitogenome with a common Chr-m2. Phylogenetic analyses based on mtDNA structures and chloroplast gene sequences both inferred that G1-G3, representing >90% of cultigens, likely inherited cytoplasm from the ancestor of domestic soybean, while G4 and G5 likely inherited cytoplasm from wild soybeans carrying GSa- and GSe-like cytoplasm through interspecific hybridization, offering new insights into soybean cultivation history.
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Affiliation(s)
- Hao Liu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Junping Yu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Xiaoxia Yu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Dan Zhang
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Han Chang
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Wei Li
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Haifeng Song
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Zheng Cui
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Peng Wang
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yixin Luo
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Fei Wang
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Dagang Wang
- Key Laboratory of Crop Quality Improvement of Anhui Province, Anhui Academy of Agricultural Sciences, Crop Research Institute, Hefei, Anhui, 230031, China
| | - Zhi Li
- Fuyang Academy of Agricultural Sciences, Fuyang, Anhui, 236000, China
| | - Zhiping Huang
- Key Laboratory of Crop Quality Improvement of Anhui Province, Anhui Academy of Agricultural Sciences, Crop Research Institute, Hefei, Anhui, 230031, China
| | - Aigen Fu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Min Xu
- Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
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Wang W, Chen L, Wang X, Duan J, Flynn RD, Wang Y, Clark CB, Sun L, Zhang D, Wang DR, Kessler SA, Ma J. A transposon-mediated reciprocal translocation promotes environmental adaptation but compromises domesticability of wild soybeans. THE NEW PHYTOLOGIST 2021; 232:1765-1777. [PMID: 34363228 DOI: 10.1111/nph.17671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Large structural variations frequently occur in higher plants; however, the impact of such variations on plant diversification, adaptation and domestication remains elusive. Here, we mapped and characterised a reciprocal chromosomal translocation in soybeans and assessed its effects on diversification and adaptation of wild (Glycine soja) and semiwild (Glycine gracilis) soybeans, and domestication of cultivated soybean (Glycine max), by tracing the distribution of the translocation in the USDA Soybean Germplasm Collection and population genetics analysis. We demonstrate that the translocation occurred through CACTA transposon-mediated chromosomal breakage in wild soybean c. 0.34 Ma and is responsible for semisterility in translocation heterozygotes and reduces their reproductive fitness. The translocation has differentiated Continental (i.e. China and Russia) populations from Maritime (i.e. Korea and Japan) populations of G. soja and predominately adapted to cold and dry climates. Further analysis revealed that the divergence of G. max from G. soja predates the translocation event and that G. gracilis is an evolutionary intermediate between G. soja and G. max. Our results highlight the effects of a chromosome rearrangement on the processes leading to plant divergence and adaptation, and provides evidence that suggests G. gracilis, rather than G. soja, as the ancestor of cultivated soybean.
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Affiliation(s)
- Weidong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Liyang Chen
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Jingbo Duan
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Rachel D Flynn
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ying Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- College of Plant Science, Jilin University, Changchun, Jilin, 130062, China
| | - Chancelor B Clark
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Lianjun Sun
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Dajian Zhang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Diane R Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Sharon A Kessler
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
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Agrawal N, Gupta M, Atri C, Akhatar J, Kumar S, Heslop-Harrison PJS, Banga SS. Anchoring alien chromosome segment substitutions bearing gene(s) for resistance to mustard aphid in Brassica juncea-B. fruticulosa introgression lines and their possible disruption through gamma irradiation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3209-3224. [PMID: 34160642 DOI: 10.1007/s00122-021-03886-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 06/08/2021] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE Heavy doses of gamma irradiation can reduce linkage drag by disrupting large sized alien translocations and promoting exchanges between crop and wild genomes. Resistance to mustard aphid (Lipaphis erysimi) infestation was significantly improved in Brassica juncea through B. juncea-B. fruticulosa introgression. However, linkage drag caused by introgressed chromatin fragments has so far prevented the deployment of this resistance source in commercial cultivars. We investigated the patterns of donor chromatin segment substitutions in the introgression lines (ILs) through genomic in situ hybridization (GISH) coupled with B. juncea chromosome-specific oligonucleotide probes. These allowed identification of large chromosome translocations from B. fruticulosa in the terminal regions of chromosomes A05, B02, B03 and B04 in three founder ILs (AD-64, 101 and 104). Only AD-101 carried an additional translocation at the sub-terminal to intercalary position in both homologues of chromosome A01. We validated these translocations with a reciprocal blast hit analysis using shotgun sequencing of three ILs and species-specific contigs/scaffolds (kb sized) from a de novo assembly of B. fruticulosa. Alien segment substitution on chromosome A05 could not be validated. Current studies also endeavoured to break linkage drag by exposing seeds to a heavy dose (200kR) of gamma radiation. Reduction in the size of introgressed chromatin fragments was observed in many M3 plants. There was a complete loss of the alien chromosome fragment in one instance. A few M3 plants with novel patterns of chromosome segment substitutions displayed improved agronomic performance coupled with resistance to mustard aphid. SNPs in such genomic spaces should aid the development of markers to track introgressed DNA and allow application in plant breeding.
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Affiliation(s)
- Neha Agrawal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Mehak Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Sarwan Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
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Fang L, Zhao T, Hu Y, Si Z, Zhu X, Han Z, Liu G, Wang S, Ju L, Guo M, Mei H, Wang L, Qi B, Wang H, Guan X, Zhang T. Divergent improvement of two cultivated allotetraploid cotton species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1325-1336. [PMID: 33448110 PMCID: PMC8313128 DOI: 10.1111/pbi.13547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/24/2020] [Accepted: 01/03/2021] [Indexed: 05/21/2023]
Abstract
Interspecific genomic variation can provide a genetic basis for local adaptation and domestication. A series of studies have presented its role of interspecific haplotypes and introgressions in adaptive traits, but few studies have addressed their role in improving agronomic character. Two allotetraploid Gossypium species, Gossypium barbadense (Gb) and G. hirsutum (Gh) originating from the Americas, are cultivated independently. Here, through sequencing and the comparison of one GWAS panel in 229 Gb accessions and two GWAS panels in 491 Gh accessions, we found that most associated loci or functional haplotypes for agronomic traits were highly divergent, representing the strong divergent improvement between Gb and Gh. Using a comprehensive interspecific haplotype map, we revealed that six interspecific introgressions from Gh to Gb were significantly associated with the phenotypic performance of Gb, which could explain 5%-40% of phenotypic variation in yield and fibre qualities. In addition, three introgressions overlapped with six associated loci in Gb, indicating that these introgression regions were under further selection and stabilized during improvement. A single interspecific introgression often possessed yield-increasing potential but decreased fibre qualities, or the opposite, making it difficult to simultaneously improve yield and fibre qualities. Our study not only has proved the importance of interspecific functional haplotypes or introgressions in the divergent improvement of Gb and Gh, but also supports their potential value in further human-mediated hybridization or precision breeding.
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Affiliation(s)
- Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Xiefei Zhu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Guizhen Liu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
- Henan Province Seed StationZhengzhouChina
| | - Sen Wang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
- Institute of Food CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Longzhen Ju
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Menglan Guo
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Huan Mei
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Luyao Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Bowen Qi
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Heng Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor. Nat Commun 2021; 12:3604. [PMID: 34127667 PMCID: PMC8203738 DOI: 10.1038/s41467-021-23879-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach.
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Zhao N, Ding X, Lian T, Wang M, Tong Y, Liang D, An Q, Sun S, Jackson SA, Liu B, Xu C. The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean. Front Genet 2020; 11:601003. [PMID: 33363574 PMCID: PMC7753205 DOI: 10.3389/fgene.2020.601003] [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: 08/31/2020] [Accepted: 11/04/2020] [Indexed: 12/22/2022] Open
Abstract
Regulatory changes include divergence in both cis-elements and trans-factors, which play roles in organismal evolution. Whole genome duplications (WGD) followed by diploidization are a recurrent feature in the evolutionary history of angiosperms. Prior studies have shown that duplicated genes have different evolutionary fates due to variable selection constraints and results in genomic compositions with hallmarks of paleopolyploidy. The recent sequential WGDs and post-WGD evolution in the common ancestor of cultivated soybean (Glycine max) and wild soybean (Glycine soja), together with other models of gene duplication, have resulted in a highly duplicated genome. In this study, we investigated the transcriptional changes in G. soja and G. max. We identified a sizable proportion of interspecific differentially expressed genes (DEGs) and found parental expression level dominance of G. max in their F1 hybrids. By classifying genes into different regulatory divergence types, we found the trans-regulatory changes played a predominant role in transcriptional divergence between wild and cultivated soybean. The same gene ontology (GO) and protein family (Pfam) terms were found to be over-represented in DEGs and genes of cis-only between JY47 and GS, suggesting the substantial contribution of cis-regulatory divergences to the evolution of wild and cultivated soybeans. By further dissecting genes into five different duplication modes, we found genes in different duplication modes tend to accumulate different types of regulatory differences. A relatively higher proportion of cis-only regulatory divergences was detected in singleton, dispersed, proximal, and tandem duplicates than WGD duplicates and genome-wide level, which is in line with the prediction of gene balance hypothesis for the differential fates of duplicated genes post-WGD. The numbers of cis-only and trans-only regulated genes were similar for singletons, whereas there were more genes of trans-only than cis-only in the rest duplication types, especially in WGD in which there were two times more trans-only genes than that in cis-only type. Tandem duplicates showed the highest proportion of trans-only genes probably due to some special features of this class. In summary, our results demonstrate that genes in different duplication modes have different fates in transcriptional evolution underpinned by cis- or trans-regulatory divergences in soybean and likely in other paleopolyploid higher organisms.
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Affiliation(s)
- Na Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun, China.,Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaoyang Ding
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Taotao Lian
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Meng Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yan Tong
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Di Liang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Qi An
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Siwen Sun
- Department of Agronomy, Jilin Agricultural University, Changchun, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Hao C, Jiao C, Hou J, Li T, Liu H, Wang Y, Zheng J, Liu H, Bi Z, Xu F, Zhao J, Ma L, Wang Y, Majeed U, Liu X, Appels R, Maccaferri M, Tuberosa R, Lu H, Zhang X. Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China. MOLECULAR PLANT 2020; 13:1733-1751. [PMID: 32896642 DOI: 10.1016/j.molp.2020.09.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 05/18/2023]
Abstract
Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes. More than 3000 wheat cultivars have been registered, released, and documented since 1949 in China. In this study, a set of 145 elite cultivars selected from historical points of wheat breeding in China were re-sequenced. A total of 43.75 Tb of sequence data were generated with an average read depth of 17.94× for each cultivar, and more than 60.92 million SNPs and 2.54 million InDels were captured, based on the Chinese Spring RefSeq genome v1.0. Seventy years of breeder-driven selection led to dramatic changes in grain yield and related phenotypes, with distinct genomic regions and phenotypes targeted by different breeders across the decades. There are very clear instances illustrating how introduced Italian and other foreign germplasm was integrated into Chinese wheat programs and reshaped the genomic landscape of local modern cultivars. Importantly, the resequencing data also highlighted significant asymmetric breeding selection among the three sub-genomes: this was evident in both the collinear blocks for homeologous chromosomes and among sets of three homeologous genes. Accumulation of more newly assembled genes in newer cultivars implied the potential value of these genes in breeding. Conserved and extended sharing of linkage disequilibrium (LD) blocks was highlighted among pedigree-related cultivars, in which fewer haplotype differences were detected. Fixation or replacement of haplotypes from founder genotypes after generations of breeding was related to their breeding value. Based on the haplotype frequency changes in LD blocks of pedigree-related cultivars, we propose a strategy for evaluating the breeding value of any given line on the basis of the accumulation (pyramiding) of beneficial haplotypes. Collectively, our study demonstrates the influence of "founder genotypes" on the output of breeding efforts over many decades and also suggests that founder genotype perspectives are in fact more dynamic when applied in the context of modern genomics-informed breeding.
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Affiliation(s)
- Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengzhi Jiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuquan Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Zheng
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hong Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhihong Bi
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Fengfeng Xu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lin Ma
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yamei Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Uzma Majeed
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing 100083, China.
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Gudi S, Atri C, Goyal A, Kaur N, Akhtar J, Mittal M, Kaur K, Kaur G, Banga SS. Physical mapping of introgressed chromosome fragment carrying the fertility restoring (Rfo) gene for Ogura CMS in Brassica juncea L. Czern & Coss. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2949-2959. [PMID: 32661588 DOI: 10.1007/s00122-020-03648-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/01/2020] [Indexed: 05/18/2023]
Abstract
Rfo is located on a radish chromosome fragment (~ 108 Kb), which is seated in the middle of a pretty large C genome translocation at the distal region of chromosome A09 of B. juncea. Ogura cytoplasmic male sterility (CMS) is used to produce hybrids in Indian mustard (Brassica juncea L.). Fertility restorers for this CMS were developed by cross-hybridizing B. juncea (AABB; 2n = 36) with B. napus (AACC; 2n = 38) carrying radish Rfo gene. This hybrid production system is normally stable, but many commercial mustard hybrids show male sterile contaminants. We aimed to identify linkage drag associated with Rfo by comparing hybridity levels of 295 handmade CMS x Rfo crosses. Although Rfo was stably inherited, hybridity was < 85 percent in several combinations. Genome re-sequencing of five fertility restorers, mapping sequencing reads to B. juncea reference and synteny analysis with Raphanus sativus D81Rfo genomic region (AJ550021.2) helped to detect ~ 108 Kb of radish chromosome (R) fragment substitution in all fertility restorers. This radish segment substitution was itself located amidst a large C genome translocation on the terminal region of chromosome A09 of B. juncea. The size of alien segment substitution varied from 11.3 (NTCN-R9) to 22.0 Mb (NAJR-102B-R). We also developed an in silico SSR map for chromosome A09 and identified many homoeologous A to the C genome exchanges in the introgressed region. A to the R genome exchanges were rare. Annotation of the substituted fragment showed the gain of many novel genes from R and C genomes and the loss of B. juncea genes from the corresponding region. We have developed a KASPar marker for marker-aided transfer of Rfo and testing hybridity levels in seed production lots.
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Affiliation(s)
- Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Javed Akhtar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Kawalpreet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gurpreet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
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Khan G, Franco FF, Silva GAR, Bombonato JR, Machado M, Alonso DP, Ribolla PEM, Albach DC, Moraes EM. Maintaining genetic integrity with high promiscuity: Frequent hybridization with low introgression in multiple hybrid zones of Melocactus (Cactaceae). Mol Phylogenet Evol 2019; 142:106642. [PMID: 31605812 DOI: 10.1016/j.ympev.2019.106642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 09/27/2019] [Accepted: 10/06/2019] [Indexed: 10/25/2022]
Abstract
Hybridization and introgression between species in contact/hybrid zones provide important insight into the genetic and ecological mechanisms of speciation. Cactaceae represents the most important radiation of true succulent angiosperms in the New World. This diversification continues to date, with species experiencing few intrinsic barriers to gene flow and the frequent occurrence of natural hybridization. Here, we used RAD-Seq single-nucleotide polymorphism (SNP) data to investigate the genetic architecture of hybridization in four hybrid zones hosting Melocactus concinnus and four congeneric species (M. ernestii, M. glaucescens, M. paucispinus, and M. zehntneri). Our results revealed that M. concinnus is highly promiscuous in sympatric areas and hybridizes with various species distributed in Morro do Chapéu (Diamantina Plateau, Bahia), eastern Brazil. However, the contemporary genomic introgression among the investigated species is very low (c. 2-5%), confirming that even in the face of hybridization, Melocactus species maintain their genetic integrity. The genomic cline approach showed a large fraction of loci deviating from a model of neutral introgression, where most of the loci are consistent with selection favoring parental genotypes. Our results suggest the occurrence of weak premating but strong postmating reproductive isolation in the analyzed cactus species. Furthermore, as most of the Melocactus species are restricted in distribution, hybridization might negatively affect their integrity if hybrids replace the parental species.
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Affiliation(s)
- Gulzar Khan
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil
| | - Fernando F Franco
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil
| | - Gislaine A R Silva
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil
| | - Juliana R Bombonato
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil; Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Programa de Pós-graduação em Biologia Comparada, Brazil
| | - Marlon Machado
- Universidade Estadual de Feira de Santana, Bahia, Brazil
| | - Diego P Alonso
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), São Paulo State University (UNESP), Sao Paulo, Brazil
| | - Paulo E M Ribolla
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), São Paulo State University (UNESP), Sao Paulo, Brazil
| | - Dirk C Albach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Germany
| | - Evandro M Moraes
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil.
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