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Li T, Xu H, Teng S, Suo M, Bahitwa R, Xu M, Qian Y, Ramstein GP, Song B, Buckler ES, Wang H. Modeling 0.6 million genes for the rational design of functional cis-regulatory variants and de novo design of cis-regulatory sequences. Proc Natl Acad Sci U S A 2024; 121:e2319811121. [PMID: 38889146 PMCID: PMC11214048 DOI: 10.1073/pnas.2319811121] [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: 11/12/2023] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
Rational design of plant cis-regulatory DNA sequences without expert intervention or prior domain knowledge is still a daunting task. Here, we developed PhytoExpr, a deep learning framework capable of predicting both mRNA abundance and plant species using the proximal regulatory sequence as the sole input. PhytoExpr was trained over 17 species representative of major clades of the plant kingdom to enhance its generalizability. Via input perturbation, quantitative functional annotation of the input sequence was achieved at single-nucleotide resolution, revealing an abundance of predicted high-impact nucleotides in conserved noncoding sequences and transcription factor binding sites. Evaluation of maize HapMap3 single-nucleotide polymorphisms (SNPs) by PhytoExpr demonstrates an enrichment of predicted high-impact SNPs in cis-eQTL. Additionally, we provided two algorithms that harnessed the power of PhytoExpr in designing functional cis-regulatory variants, and de novo creation of species-specific cis-regulatory sequences through in silico evolution of random DNA sequences. Our model represents a general and robust approach for functional variant discovery in population genetics and rational design of regulatory sequences for genome editing and synthetic biology.
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Affiliation(s)
- Tianyi Li
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Hui Xu
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Shouzhen Teng
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Mingrui Suo
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Revocatus Bahitwa
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
- Legumes Research Program, Research and Innovation Division, Tanzania Agricultural Research Institute, Ilonga, Kilosa, Morogoro67410, Tanzania
| | - Mingchi Xu
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Yiheng Qian
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Guillaume P. Ramstein
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus8000, Denmark
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, People’s Republic of China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi712100, People’s Republic of China
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY14853
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY14853
| | - Hai Wang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing100193, People’s Republic of China
- Sanya Institute of China Agricultural University, Sanya572025, People’s Republic of China
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Sood S, Bhardwaj V, Mangal V, Kardile H, Dipta B, Kumar A, Singh B, Siddappa S, Sharma AK, Dalamu, Buckseth T, Chaudhary B, Kumar V, Pandey N. Development of near homozygous lines for diploid hybrid TPS breeding in potatoes. Heliyon 2024; 10:e31507. [PMID: 38831819 PMCID: PMC11145485 DOI: 10.1016/j.heliyon.2024.e31507] [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: 09/20/2023] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Diploid inbred-based F1 hybrid True Potato Seed (DHTPS) breeding is a novel technique to transform potato breeding and cultivation across the globe. Significant efforts are being made to identify elite diploids, dihaploids and develop diploid inbred lines for heterosis exploitation in potatoes. Self-incompatibility is the first obstacle for developing inbred lines in diploid potatoes, which necessitates the introgression of a dominant S locus inhibitor gene (Sli) for switching self-incompatibility to self-compatibility. We evaluated a set of 357 diploid clones in different selfing generations for self-compatibility and degree of homozygosity using Kompetitive Allele Specific PCR (KASP) Single Nucleotide Polymorphism (SNP) markers. A subset of 10 KASP markers of the Sli candidate region on chromosome 12 showed an association with the phenotype for self-compatibility. The results revealed that the selected 10 KASP markers for the Sli gene genotype could be deployed for high throughput rapid screening of self-compatibility in diploid populations and to identify new sources of self-compatibility. The homozygosity assessed through 99 KASP markers distributed across all the chromosomes of the potato genome was 20-78 % in founder diploid clones, while different selfing generations, i.e., S0, S1, S2 and S3 observed 36.1-80.4, 56.9-82.8, 59.5-85.4 and 73.7-87.8 % average homozygosity, respectively. The diploid plants with ∼80 % homozygosity were also observed in the first selfing generation, which inferred that homozygosity assessment in the early generations itself could identify the best plants with high homozygosity to speed up the generation of diploid inbred lines.
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Affiliation(s)
- Salej Sood
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Hemant Kardile
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Bhawna Dipta
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Ashwani Kumar
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Baljeet Singh
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | | | | | - Dalamu
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Tanuja Buckseth
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Babita Chaudhary
- ICAR-Central Potato Research Institute, Regional Station, Modipuram, UP, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - N.K. Pandey
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
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Liu S, Cheng H, Zhang Y, He M, Zuo D, Wang Q, Lv L, Lin Z, Liu J, Song G. Cotton transposon-related variome reveals roles of transposon-related variations in modern cotton cultivation. J Adv Res 2024:S2090-1232(24)00209-1. [PMID: 38810909 DOI: 10.1016/j.jare.2024.05.019] [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: 12/27/2023] [Revised: 03/26/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024] Open
Abstract
INTRODUCTION Transposon plays a vital role in cotton genome evolution, contributing to the expansion and divergence of genomes within the Gossypium genus. However, knowledge of transposon activity in modern cotton cultivation is limited. OBJECTIVES In this study, we aimed to construct transposon-related variome within Gossypium genus and reveal role of transposon-related variations during cotton cultivation. In addition, we try to identify valuable transposon-related variations for cotton breeding. METHODS We utilized graphical genome construction to build up the graphical transposon-related variome. Based on the graphical variome, we integrated t-test, eQTL analysis and Mendelian Randomization (MR) to identify valuable transposon activities and elite genes. In addition, a convolutional neural network (CNN) model was constructed to evaluate epigenomic effects of transposon-related variations. RESULTS We identified 35,980 transposon activities among 10 cotton genomes, and the diversity of genomic and epigenomic features was observed among 21 transposon categories. The graphical cotton transposon-related variome was constructed, and 9,614 transposon-related variations with plasticity in the modern cotton cohort were used for eQTL, phenotypic t-test and Mendelian Randomization. 128 genes were identified as gene resources improving fiber length and strength simultaneously. 4 genes were selected from 128 genes to construct the elite gene panel whose utility has been validated in a natural cotton cohort and 2 accessions with phenotypic divergence. Based on the eQTL analysis results, we identified transposon-related variations involved in cotton's environmental adaption and human domestication, providing evidence of their role in cotton's adaption-domestication cooperation. CONCLUSIONS The cotton transposon-related variome revealed the role of transposon-related variations in modern cotton cultivation, providing genomic resources for cotton molecular breeding.
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Affiliation(s)
- Shang Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hailiang Cheng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China
| | - Youping Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Man He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Dongyun Zuo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Qiaolian Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Limin Lv
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhongxv Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ji Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Guoli Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China.
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Ames M, Hamernik A, Behling W, Douches DS, Halterman DA, Bethke PC. A survey of the Sli gene in wild and cultivated potato. PLANT DIRECT 2024; 8:e589. [PMID: 38766508 PMCID: PMC11099725 DOI: 10.1002/pld3.589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/27/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Inbred-hybrid breeding of diploid potatoes necessitates breeding lines that are self-compatible. One way of incorporating self-compatibility into incompatible cultivated potato (Solanum tuberosum) germplasm is to introduce the S-locus inhibitor gene (Sli), which functions as a dominant inhibitor of gametophytic self-incompatibility. To learn more about Sli diversity and function in wild species relatives of cultivated potato, we obtained Sli gene sequences that extended from the 5'UTR to the 3'UTR from 133 individuals from 22 wild species relatives of potato and eight diverse cultivated potato clones. DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. DNA sequences in one group contain the 533 bp insertion upstream of the start codon identified previously in self-compatible potato. The second group lacks the insertion. Three diploid and four polyploid individuals of wild species collected from geographically disjointed localities contained Sli with the 533 bp insertion. For most of the wild species clones examined, however, Sli did not have the insertion. Phylogenetic analysis indicated that Sli sequences with the insertion, in wild species and in cultivated clones, trace back to a single origin. Some diploid wild potatoes that have Sli with the insertion were self-incompatible and some wild potatoes that lack the insertion were self-compatible. Although there is evidence of positive selection for some codon positions in Sli, there is no evidence of diversifying selection at the gene level. In silico analysis of Sli protein structure did not support the hypothesis that amino acid changes from wild-type (no insertion) to insertion-type account for changes in protein function. Our study demonstrated that genetic factors besides the Sli gene must be important for conditioning a switch in the mating system from self-incompatible to self-compatible in wild potatoes.
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Affiliation(s)
- Mercedes Ames
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Andy Hamernik
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - William Behling
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - David S. Douches
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Dennis A. Halterman
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Paul C. Bethke
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
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Liu S, Cheng H, Zhang Y, He M, Zuo D, Wang Q, Lv L, Lin Z, Song G. Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement. Genes (Basel) 2024; 15:378. [PMID: 38540437 PMCID: PMC10970022 DOI: 10.3390/genes15030378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 06/14/2024] Open
Abstract
Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort's fingerprint genomic sites. The FPFinder was developed based on the term frequency-inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these pedigree-featured sites had a role in cotton development. In addition, we applied FPFinder to evaluate the geographical bias of fiber-length-related genomic sites from a modern cotton cohort consisting of 410 accessions. Enriching elite sites in cultivars from the Yangtze River region resulted in the longer fiber length of Yangze River-sourced accessions. Apart from characterizing functional sites, we also identified 12,536 region-specific genomic sites. Combining the transcriptome data of multiple tissues and samples under various abiotic stresses, we found that several region-specific sites contributed to environmental adaptation. In this research, FPFinder revealed the role of the cotton pedigree fingerprint and region-specific sites in cotton development and environmental adaptation, respectively. The FPFinder can be applied broadly in other crops and contribute to genetic breeding in the future.
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Affiliation(s)
- Shang Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Hailiang Cheng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
- Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China
| | - Youping Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Man He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Dongyun Zuo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Qiaolian Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Limin Lv
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Zhongxv Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Guoli Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
- Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China
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Schraiber JG, Edge MD, Pennell M. Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579721. [PMID: 38496530 PMCID: PMC10942266 DOI: 10.1101/2024.02.10.579721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique-including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model-can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.
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Song B, Buckler ES, Stitzer MC. New whole-genome alignment tools are needed for tapping into plant diversity. TRENDS IN PLANT SCIENCE 2024; 29:355-369. [PMID: 37749022 DOI: 10.1016/j.tplants.2023.08.013] [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: 04/24/2023] [Revised: 07/19/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023]
Abstract
Genome alignment is one of the most foundational methods for genome sequence studies. With rapid advances in sequencing and assembly technologies, these newly assembled genomes present challenges for alignment tools to meet the increased complexity and scale. Plant genome alignment is technologically challenging because of frequent whole-genome duplications (WGDs) as well as chromosome rearrangements and fractionation, high nucleotide diversity, widespread structural variation, and high transposable element (TE) activity causing large proportions of repeat elements. We summarize classical pairwise and multiple genome alignment (MGA) methods, and highlight techniques that are widely used or are being developed by the plant research community. We also outline the remaining challenges for precise genome alignment and the interpretation of alignment results in plants.
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Affiliation(s)
- Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China; Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA; Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Michelle C Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Schreiber M, Jayakodi M, Stein N, Mascher M. Plant pangenomes for crop improvement, biodiversity and evolution. Nat Rev Genet 2024:10.1038/s41576-024-00691-4. [PMID: 38378816 DOI: 10.1038/s41576-024-00691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 02/22/2024]
Abstract
Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.
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Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, Marburg, Germany
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Liu Y, Li Y, Wang A, Xu Z, Li C, Wang Z, Guo B, Chen Y, Tang F, Li J. Enhancing cold resistance in Banana (Musa spp.) through EMS-induced mutagenesis, L-Hyp pressure selection: phenotypic alterations, biomass composition, and transcriptomic insights. BMC PLANT BIOLOGY 2024; 24:101. [PMID: 38331759 PMCID: PMC10854111 DOI: 10.1186/s12870-024-04775-5] [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: 11/03/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND The cultivation of bananas encounters substantial obstacles, particularly due to the detrimental effects of cold stress on their growth and productivity. A potential remedy that has gained attention is the utilization of ethyl mesylate (EMS)-induced mutagenesis technology, which enables the creation of a genetically varied group of banana mutants. This complex procedure entails subjecting the mutants to further stress screening utilizing L-Hyp in order to identify those exhibiting improved resistance to cold. This study conducted a comprehensive optimization of the screening conditions for EMS mutagenesis and L-Hyp, resulting in the identification of the mutant cm784, which exhibited remarkable cold resistance. Subsequent investigations further elucidated the physiological and transcriptomic responses of cm784 to low-temperature stress. RESULTS EMS mutagenesis had a substantial effect on banana seedlings, resulting in modifications in shoot and root traits, wherein a majority of seedlings exhibited delayed differentiation and limited elongation. Notably, mutant leaves displayed altered biomass composition, with starch content exhibiting the most pronounced variation. The application of L-Hyp pressure selection aided in the identification of cold-resistant mutants among seedling-lethal phenotypes. The mutant cm784 demonstrated enhanced cold resistance, as evidenced by improved survival rates and reduced symptoms of chilling injury. Physiological analyses demonstrated heightened activities of antioxidant enzymes and increased proline production in cm784 when subjected to cold stress. Transcriptome analysis unveiled 946 genes that were differentially expressed in cm784, with a notable enrichment in categories related to 'Carbohydrate transport and metabolism' and 'Secondary metabolites biosynthesis, transport, and catabolism'. CONCLUSION The present findings provide insights into the molecular mechanisms that contribute to the heightened cold resistance observed in banana mutants. These mechanisms encompass enhanced carbohydrate metabolism and secondary metabolite biosynthesis, thereby emphasizing the adaptive strategies employed to mitigate the detrimental effects induced by cold stress.
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Affiliation(s)
- Yumeng Liu
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yujia Li
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Anbang Wang
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Zhuye Xu
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- College of Horticulture, Hainan University, Haikou, 571101, Hainan, China
| | - Chunfang Li
- Collage of Tropical Crop, Yunnan Agricultural University, Puer, 611101, Yunnan, China
| | - Zuo Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Borui Guo
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Chen
- Collage of Tropical Crop, Yunnan Agricultural University, Puer, 611101, Yunnan, China
| | - Fenling Tang
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Jingyang Li
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China.
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
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10
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Luo H, Wang X, You C, Wu X, Pan D, Lv Z, Li T, Zhang D, Shen Z, Zhang X, Liu G, He K, Ye Q, Jia Y, Zhao Q, Deng X, Cao X, Song X, Huang G. Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance. SCIENCE CHINA. LIFE SCIENCES 2024; 67:149-160. [PMID: 37897613 DOI: 10.1007/s11427-023-2463-y] [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: 07/20/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023]
Abstract
Alkaline soils pose an increasing problem for agriculture worldwide, but using stress-tolerant plants as green manure can improve marginal land. Here, we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and, when used as a green manure, substantially improves alkaline soil. To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume, we generated the first telomere-to-telomere genome assembly of S. cannabina spanning ∼2,087 Mb. The assembly included all centromeric regions, which contain centromeric satellite repeats, and complete chromosome ends with telomeric characteristics. Further genome analysis distinguished A and B subgenomes, which diverged approximately 7.9 million years ago. Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events (>10 Mb) and a significant, transposon-driven size expansion of the chromosome 5A homoeolog. We further identified four specific alkali-induced phosphate transporter genes in S. cannabina; these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil. Our work highlights the significance of S. cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.
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Affiliation(s)
- Haofei Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofei Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Changqing You
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuedan Wu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Duofeng Pan
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Zhiyao Lv
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Tong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongmei Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Zhongbao Shen
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xiaodong Zhang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257345, China
- Shandong Green Manure Ecological Technology Co., Ltd, Dongying, 257345, China
| | - Guodao Liu
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Kaixuan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Qingtong Ye
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yajun Jia
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Qinghua Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Gai Huang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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11
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Comai L. Unlikely heroes on the long and winding road to potato inbreeding. ABIOTECH 2023; 4:267-271. [PMID: 37970470 PMCID: PMC10638346 DOI: 10.1007/s42994-023-00109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 11/17/2023]
Abstract
Conversion of potato from a tetraploid, heterozygous, vegetatively propagated crop to a diploid F1 hybrid, propagated via botanical seed, would constitute a considerable advance for global agriculture, but faces multiple challenges. One such challenge is the difficulty in inbreeding potato, which involves purging deleterious alleles from its genome. This commentary discusses possible reasons for this difficulty and highlights a recent sequence-based effort to classify SNP variation, in potato germplasm, according to its deleterious potential. Tools and strategies connected to this database may facilitate development of F1 hybrids.
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Affiliation(s)
- Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616 USA
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12
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Li D, Lu X, Qian D, Wang P, Tang D, Zhong Y, Shang Y, Guo H, Wang Z, Zhu G, Zhang C. Dissected Leaf 1 encodes an MYB transcription factor that controls leaf morphology in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:183. [PMID: 37555965 DOI: 10.1007/s00122-023-04430-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/24/2023] [Indexed: 08/10/2023]
Abstract
KEY MESSAGE The transcription factor StDL1 regulates dissected leaf formation in potato and the genotype frequency of recessive Stdl1/Stdl1, which results in non-dissected leaves, has increased in cultivated potatoes. Leaf morphology is a key trait of plants, influencing plant architecture, photosynthetic efficiency and yield. Potato (Solanum tuberosum L.), the third most important food crop worldwide, has a diverse leaf morphology. However, despite the recent identification of several genes regulating leaf formation in other plants, few genes involved in potato leaf development have been reported. In this study, we identified an R2R3 MYB transcription factor, Dissected Leaf 1 (StDL1), regulating dissected leaf formation in potato. A naturally occurring allele of this gene, Stdl1, confers non-dissected leaves in young seedlings. Knockout of StDL1 in a diploid potato changes the leaf morphology from dissected to non-dissected. Experiments in N. benthamiana and yeast show that StDL1 is a transcriptional activator. Notably, by calculating the genotype frequency of the Stdl1/Stdl1 in 373-potato accessions, we found that it increases significantly in cultivated potatoes. This work reveals the genetic basis of dissected leaf formation in potato and provides insights into plant leaf morphology.
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Affiliation(s)
- Dawei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xiaoyue Lu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Duoduo Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518120, China
| | - Pei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dié Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yang Zhong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650000, China
| | - Han Guo
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhen Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Guangtao Zhu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650000, China.
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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13
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Sun S, Wang B, Li C, Xu G, Yang J, Hufford MB, Ross-Ibarra J, Wang H, Wang L. Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding. Mol Biol Evol 2023; 40:msad170. [PMID: 37494285 PMCID: PMC10414807 DOI: 10.1093/molbev/msad170] [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: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than nondeleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in nondifferentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.
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Affiliation(s)
- Shichao Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, China
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14
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Agha HI, Shannon LM, Morrell PL. Unloading potatoes: Potato breeding moves forward with only half the genome. CELL GENOMICS 2023; 3:100343. [PMID: 37388910 PMCID: PMC10300581 DOI: 10.1016/j.xgen.2023.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Potato is one of the most important food crops in the world and, in contrast to other staples, has not seen large improvements in yield. Agha, Shannon, and Morrell preview an article recently published in Cell, "Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding," which advances potato breeding strategies via a genetic approach.
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Affiliation(s)
- Husain I. Agha
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55018, USA
| | - Laura M. Shannon
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55018, USA
| | - Peter L. Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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