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Plant genome resequencing and population genomics: Current status and future prospects

MOLECULAR PLANT (2023)

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Article Plant Sciences

Legume-wide comparative analysis of pod shatter locus PDH1 reveals phaseoloid specificity, high cowpea expression, and stress responsive genomic context

Jacob Marsh et al.

Summary: Pod dehiscence is a major cause of yield loss in legumes, especially under arid conditions. This study investigates the evolution of the Pod indehiscent 1 (PDH1) gene in legumes and its role in controlling pod dehiscence. The results reveal the presence of PDH1 orthologs in certain legume species and the absence of PDH1 in Cajanus cajan, suggesting its contribution to indehiscence in this species. Additionally, the study identifies a novel PDH1 ortholog in Vigna angularis and highlights the potential influence of transcription factors and signaling gene families in regulating PDH1 expression under specific environmental conditions. These findings provide valuable insights into the evolutionary history of PDH1 and its potential application in optimizing pod dehiscence in legume crops.

PLANT JOURNAL (2023)

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Article Multidisciplinary Sciences

Dual domestications and origin of traits in grapevine evolution

Yang Dong et al.

Summary: We investigate the evolution and domestication of grapevines by studying 3525 cultivated and wild varieties worldwide. Harsh climate in the Pleistocene led to the separation of wild grape ecotypes due to habitat fragmentation. Domestication occurred around 11,000 years ago in Western Asia and the Caucasus, giving rise to table and wine grapevines. The domesticates from Western Asia dispersed into Europe, hybridizing with ancient wild ecotypes and diversifying into muscat and unique western wine grape ancestries as human migration took place in the late Neolithic. Analysis of domestication traits also provides insights into the selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These findings demonstrate the significance of grapevines in the early development of agriculture across Eurasia.

SCIENCE (2023)

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Article Plant Sciences

Diversity of fatty acid biosynthesis genes across the soybean pangenome

Mark C. C. Derbyshire et al.

Summary: This study analyzes the soybean pangenome to identify fatty acid biosynthesis genes and their sequence diversity. It finds possible instances of gene missing in wild soybean and identifies missense variants in fatty acid biosynthesis genes. The frequency of these variants has been significantly reduced during domestication.

PLANT GENOME (2023)

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Article Multidisciplinary Sciences

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing

Peng Ni et al.

Summary: The authors develop a deep learning tool ccsmeth and a Nextflow pipeline ccsmethphase for accurate detection and phasing of DNA 5mCpG using CCS reads in human. Existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. By training ccsmeth with PacBio CCS reads, the authors achieve high accuracy in 5mCpG detection at single-molecule resolution and strong correlations with bisulfite sequencing and nanopore sequencing at the genome-wide level.

NATURE COMMUNICATIONS (2023)

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Article Biochemistry & Molecular Biology

Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis

Yu Zhang et al.

Plant Communications (2023)

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Article Biochemistry & Molecular Biology

Genomic footprints of sorghum domestication and breeding selection for multiple end uses

Xiaoyuan Wu et al.

Summary: This study conducted population genomics analyses on a global collection of sorghum accessions and revealed frequent genetic exchanges and strong selective sweeps in the sorghum genome. The study also identified different models of haplotype changes in domestication genes and demonstrated an unconscious selection of a gene during the improvement of grain sorghum.

MOLECULAR PLANT (2022)

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Article Multidisciplinary Sciences

Green plant genomes: What we know in an era of rapidly expanding opportunities

W. John Kress et al.

Summary: Green plants are essential to ecosystems, human health, and agriculture, but generating and storing their genomes is a major challenge. Currently, there are fewer than 300 complete chromosome-scale genome assemblies for green plants, representing less than 900 species. Many species, especially those from extreme environments, still lack suitable tissue samples for genomic sequencing. The annotation of plant genomes also needs improvement.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Agronomy

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Jacob Marsh et al.

Summary: This study characterized the major high-protein/low-oil associated locus cqProt-003 in soybeans by analyzing the haplotype diversity and global distribution. The results revealed that a 304 bp deletion and variable tandem repeats in the protein coding regions are likely causal candidates. It was found that the high-protein haplotype is common in wild accessions, rare in landraces, and near absent in cultivated breeding pools, suggesting a correlation with domestication and improvement.

THEORETICAL AND APPLIED GENETICS (2022)

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Review Plant Sciences

Twenty years of plant genome sequencing: achievements and challenges

Yanqing Sun et al.

Summary: The publication of plant genome sequences has advanced research in plant biology and provided crucial information for crop breeding.

TRENDS IN PLANT SCIENCE (2022)

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Article Plant Sciences

Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs

Silvia F. Zanini et al.

Summary: Advances in high-throughput DNA sequencing technologies have facilitated crop pangenome studies, providing more accurate genetic variation information and aiding in the detection and annotation of complex DNA polymorphisms like structural variations. The potential of pangenomes in discovering and characterizing noncoding regulatory sequences and their variations is highlighted, with an outlook on innovative data structures representing the complete content of plant pangenomes.

PLANT GENOME (2022)

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Article Plant Sciences

Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction

Mitchell Gill et al.

Summary: Recent growth in crop genomic and trait data has provided opportunities for faster crop improvement. Research shows that machine learning outperforms deep learning in genotype to phenotype prediction, and identified loci overlap with GWAS and previous studies. Feature importance rankings can reduce marker input and maintain or improve prediction performance.

BMC PLANT BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

Cassandria Geraldine Tay Fernandez et al.

Summary: Pangenomes are a valuable resource for studying genomic variation within species, but many under-utilised crop species still lack pangenome data. Establishing pangenomes for these species is crucial for their improvement as they are important food sources.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

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Article Genetics & Heredity

Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding

Jihong Hu et al.

Summary: This study conducted whole-genome resequencing of 418 diverse rapeseed accessions and performed genome-wide association analyses for 56 agronomic traits. It provides insights into the genetic basis for the selection of adaptation and agronomic traits in rapeseed breeding.

NATURE GENETICS (2022)

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Article Plant Sciences

The pangenome of banana highlights differences between genera and genomes

Habib Rijzaani et al.

Summary: Banana from the Musaceae family has a complex genetic history, with different cultivated clones belonging to the Musa genus and Ensete species. The study presents the first cross-genus pangenome of banana, identifying genes that differentiate between species and potentially supporting breeding programs.

PLANT GENOME (2022)

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Article Plant Sciences

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

Philipp E. Bayer et al.

Summary: Plant gene content varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding leads to changes in gene and allele frequency, with a reduction in genetic diversity and a decrease in the average number of protein-coding genes per individual. However, some genes and allelic variants increase in frequency due to selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in soybean.

PLANT GENOME (2022)

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Article Plant Sciences

Wheat Panache: A pangenome graph database representing presence-absence variation across sixteen bread wheat genomes

Philipp E. Bayer et al.

Summary: Bread wheat is a vital crop with a complex genome, making genomic approaches for improvement challenging. To address this, a wheat pangenome graph database has been developed for visualization and comparison of wheat genomes.

PLANT GENOME (2022)

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Article Biochemical Research Methods

Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames

Mengyun Jiang et al.

Summary: Accurate prediction of ORFs is essential for studying and utilizing genome sequences. This study introduces a novel approach utilizing nucleotide periodicity in populational genomic variants to predict ORFs and develops the OrfPP software package for validation. The method demonstrates high accuracy and reliability in various complex genomes.

BRIEFINGS IN BIOINFORMATICS (2022)

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Review Plant Sciences

Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies

Soodeh Tirnaz et al.

Summary: Global agricultural industries are facing pressure to meet future food demand, but the existing crop genetic diversity may not be sufficient. However, advances in genome sequencing technologies and discovery of genetic diversity in crop wild relatives (CWRs) offer potential for crop improvement. There are various ex-situ and in-situ resources holding rare and valuable wild species, which carry agronomically important traits. The availability and use of CWR genomic resources, as well as modern breeding experimental approaches and computational methods, can contribute to crop adaptability and yield improvement.

FRONTIERS IN PLANT SCIENCE (2022)

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Article Multidisciplinary Sciences

Graph pangenome captures missing heritability and empowers tomato breeding

Yao Zhou et al.

Summary: Constructing a graph pangenome of tomato can improve the estimation of heritability for complex traits, identify more causal structural variants, and facilitate the identification of genetic factors underlying agronomically important traits. This study advances our understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.

NATURE (2022)

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Article Multidisciplinary Sciences

Genome evolution and diversity of wild and cultivated potatoes

Die Tang et al.

Summary: This study assembles 44 high-quality diploid potato genomes to investigate the genome evolution and diversity of potatoes. The results show a substantial expansion of disease-resistance genes in the potato genome compared to related solanaceous crops, indicating the impact of tuber-based propagation strategies on potato genome evolution. The study also identifies a transcription factor that determines tuber identity and its interaction with an inductive signal.

NATURE (2022)

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Editorial Material Genetics & Heredity

Graph pangenomes find missing heritability

David Edwards et al.

Summary: The use of association studies to identify candidate genes for complex traits in plants has been challenging, but graphical pangenomes and the identification of causal variants help overcome this issue and provide important advances for crop breeding.

NATURE GENETICS (2022)

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Article Plant Sciences

HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables

Cong Feng et al.

Summary: Haplotype identification, characterization, and visualization are crucial in population genomics. HAPPE is a user-friendly tool that uses coloring of Excel tables to display genotypes and haplotypes, along with additional information such as phylogenetic trees and GWAS values.

FRONTIERS IN PLANT SCIENCE (2022)

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Review Plant Sciences

Pangenomics and Crop Genome Adaptation in a Changing Climate

Jakob Petereit et al.

Summary: Climate change will impact crop productivity, and agriculture needs to adapt to support future food production. Wild plant species may have genes that can support crop adaptation to changing environments. By identifying individuals with enhanced climate resilience, we can understand the genomic basis for this resilience and apply it to crop breeding.

PLANTS-BASEL (2022)

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Article Evolutionary Biology

Whole-genome resequencing reveals signature of local adaptation and divergence in wild soybean

Jiao Wang et al.

Summary: Genome sequencing of wild soybean in China reveals the genomic basis of local adaptation and provides valuable resources for climate-smart crop breeding.

EVOLUTIONARY APPLICATIONS (2022)

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Editorial Material Biochemistry & Molecular Biology

Gregor Mendel: The father of genetics who opened a biological world full of wonders

Shifeng Cheng

MOLECULAR PLANT (2022)

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Article Plant Sciences

Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm

Ainong Shi et al.

Summary: This study identified 9 SNP markers associated with white rust resistance in spinach through genome-wide associating study and performed genomic prediction with high prediction accuracy of 0.84. These markers and the high prediction accuracy are valuable for improving spinach through marker-assisted selection and genomic selection.

HORTICULTURE RESEARCH (2022)

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Article Multidisciplinary Sciences

Genomic basis of geographical adaptation to soil nitrogen in rice

Yongqiang Liu et al.

Summary: This study uncovers the genetic basis of nitrogen-use efficiency in rice, specifically related to tillering response to nitrogen, and identifies OsTCP19 as a key regulator modulating this response. The differential transcriptional response and variation in tillering response to nitrogen among rice varieties are governed by a 29-bp insertion and/or deletion in the OsTCP19 promoter, with implications for geographical adaptation in rice and potential for breeding high-yielding, nitrogen-efficient modern rice cultivars.

NATURE (2021)

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Article Multidisciplinary Sciences

Genome-wide detection of cytosine methylation by single molecule real-time sequencing

O. Y. Olivia Tse et al.

Summary: The study developed a methodology for direct detection of S-Methylcytosine, achieving genome-wide SmC detection at single-base resolution in various biological samples with high sensitivity and specificity. It also allowed for the measurement of allele-specific methylation patterns in imprinted genes.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Multidisciplinary Sciences

Efficient assembly of nanopore reads via highly accurate and intact error correction

Ying Chen et al.

Summary: The error correction and de novo assembly tool NECAT developed by the authors efficiently produces high-quality assemblies of nanopore reads. The tool utilizes adaptive read selection and a two-step progressive method to overcome the high error rates in nanopore reads.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

A chickpea genetic variation map based on the sequencing of 3,366 genomes

Rajeev K. Varshney et al.

Summary: By studying the genetic diversity of chickpea, the research team estimated the divergence of Cicer over the last 21 million years and identified chromosomal locations of deleterious mutations in elite germplasm. They also found targets for purging deleterious alleles through genomics-assisted breeding and proposed three crop breeding strategies.

NATURE (2021)

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Article Multidisciplinary Sciences

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

John T. Lovell et al.

Summary: Climate change and environmental extremes threaten food and fuel security, as well as global crop productivity. Molecular and adaptive breeding strategies can help improve crop resilience, but require in-depth knowledge of productivity and adaptation genes. The study on the genome of switchgrass revealed extensive genomic evidence of climate adaptation and accelerated climate adaptation through gene flow during postglacial colonization. These findings not only provide insights into climate adaptation patterns, but also offer tools for breeders to increase switchgrass yield for sustainable bioenergy production.

NATURE (2021)

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Article Genetics & Heredity

A quantitative genomics map of rice provides genetic insights and guides breeding

Xin Wei et al.

Summary: The study emphasizes the importance of genetic diversity in rice breeding by providing a comprehensive map of rice quantitative trait nucleotides (QTNs) and their effects. Population genetic analyses reveal associations between QTN allele frequency changes and domestication, local adaptation, and heterosis. The development of a genome navigation system, RiceNavi, offers an efficient platform for rice breeding.

NATURE GENETICS (2021)

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Article Multidisciplinary Sciences

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

Jouni Siren et al.

Summary: Giraffe is a pangenome short-read mapper that efficiently maps to a collection of haplotypes threaded through a sequence graph. It speeds up mapping to thousands of human genomes and enables improved accuracy in genome-wide genotyping, ultimately enhancing genomic analyses. This tool facilitates a more comprehensive characterization of variation and has the potential to benefit various genomic studies.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean

Tatiana Garcia et al.

Summary: Lima bean, an important crop for food security in Latin America and elsewhere, has been studied for its genome assembly, population genomics analysis using genotyping-by-sequencing data, and identification of key genes related to disease resistance and seed development through RNA-seq analysis.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Genome-wide association studies provide insights into the genetic determination of fruit traits of pear

Ming-Yue Zhang et al.

Summary: This study conducted genome-wide association studies to identify loci associated with fruit quality and phenological traits in pear, revealing continuous selection pressure on important traits during breeding. The candidate gene PbrSTONE was functionally verified to play a key role in regulating stone cell formation, a critical fruit quality trait in pear.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits

Xiaofeng Cai et al.

Summary: This study presents a high-quality reference genome assembly of spinach and population genomic analyses, shedding light on genome rearrangements during spinach domestication and the impact of artificial selection on spinach phenotypic evolution. This research also identifies domestication sweeps in the spinach genome associated with important traits, providing valuable resources for spinach breeding.

NATURE COMMUNICATIONS (2021)

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Article Environmental Sciences

Maize Yield Prediction at an Early Developmental Stage Using Multispectral Images and Genotype Data for Preliminary Hybrid Selection

Monica F. Danilevicz et al.

Summary: The study presents a multimodal deep learning model for early prediction of maize performance using multispectral data and vegetation indices. The model accurately predicted yield and identified high-yielding varieties, outperforming previous models. Inclusion of vegetation indices improved model performance, providing a decision support tool for identifying promising lines early in the field trial.

REMOTE SENSING (2021)

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Article Biochemistry & Molecular Biology

Unraveling a genetic roadmap for improved taste in the domesticated apple

Liao Liao et al.

Summary: The study revealed the genetic basis of fruit taste in apples and its evolution during domestication, identifying several candidate genes for genetic manipulation of fruit quality.

MOLECULAR PLANT (2021)

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Article Genetics & Heredity

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits

Doruk Beyter et al.

Summary: Analysis of long-read sequencing data from 3,622 Icelanders identifies a set of high-confidence structural variants and provides insights into their effect on human traits and diseases.

NATURE GENETICS (2021)

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Article Genetics & Heredity

Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce

Tong Wei et al.

Summary: This study conducted whole-genome resequencing of 445 Lactuca accessions, including major lettuce crop types and wild relative species, providing a comprehensive map of lettuce genome variations and shedding light on the domestication history of cultivated lettuce. The research revealed that lettuce was first domesticated near the Caucasus, marked by loss of seed shattering, and identified the genetic architecture of other domestication traits and wild introgressions in major resistance clusters in the lettuce genome. This study offers valuable genomic resources for crop breeding and contributes to a better understanding of the domestication history of cultivated lettuce.

NATURE GENETICS (2021)

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Review Agronomy

Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics

Jacob I. Marsh et al.

Summary: The translation of research findings into climate smart crops in the field relies on advances in bioinformatics to harness data from vast phenomics and genomics datasets. High-throughput phenotyping and genomics technologies play a crucial role in providing information for guiding the breeding of climate smart crops adapted to the environment. Bioinformatics is essential for integrating and exploiting the accumulating wealth of data for detection of genomic targets underlying key adaptive climate-resilient traits.

THEORETICAL AND APPLIED GENETICS (2021)

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Article Biochemistry & Molecular Biology

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Peng Qin et al.

Summary: The study assembled high-quality genomes of genetically diverse rice accessions, discovering a large number of structural variations and gene copy number variations. By using a graph-based genome, the research explored the impact of these variations on rice domestication and environmental adaptation.

CELL (2021)

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Review Biochemistry & Molecular Biology

Genome-wide association studies: assessing trait characteristics in model and crop plants

Saleh Alseekh et al.

Summary: GWAS is a successful method for studying genotype-phenotype associations, initially developed in human disease genetics and now widely embraced in plant research. Plant GWAS has been applied in model and crop species over the past decade, covering various fields such as biotic resistance, abiotic tolerance, yield-associated traits, and metabolic composition.

CELLULAR AND MOLECULAR LIFE SCIENCES (2021)

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Article Biochemistry & Molecular Biology

Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees

Xia Wang et al.

Summary: The study found genetic differentiation between Tibetan peaches at different altitudes, with genes associated with light stress signaling enriched in differentiated regions. Phenylpropanoids were found to be positively correlated with altitudes. Specific SINE retrotransposons were identified in Tibetan peaches, playing a role in promoting the accumulation of beneficial metabolites for adaptation to harsh environments in the Himalayan region.

CURRENT BIOLOGY (2021)

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Article Genetics & Heredity

High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement

Zhiying Ma et al.

Summary: The study generated high-quality genomes of two cultivated cotton species and analyzed the distribution of structural variations in different subgenomes, discovering structural variations that influence agronomic traits. The findings provide insights into the role of structural variations in genotype-to-phenotype relationships and their potential utility in crop improvement.

NATURE GENETICS (2021)

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Article Genetics & Heredity

Genomic insights into the origin, domestication and diversification of Brassica juncea

Lei Kang et al.

Summary: This study presents a chromosome-scale de novo assembly of a yellow-seeded Brassica juncea genome and population analyses of 480 accessions from 38 countries, shedding light on the origin, domestication history, and morphological diversification of B. juncea. The research supports the hypothesis that B. juncea most likely originated in West Asia 8,000-14,000 years ago via natural interspecific hybridization, and new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations, and tissue-specific RNA-sequencing analysis provide insights into the domestication history of flowering time and seed weight, as well as human selection for morphological diversification in this versatile species.

NATURE GENETICS (2021)

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Article Plant Sciences

Integrating genomics and multiplatform metabolomics enables metabolite quantitative trait loci detection in breeding-relevant apple germplasm

Emma A. Bilbrey et al.

Summary: The study utilized a high-throughput integration strategy to investigate genotype-phytochemical associations in apples, identifying multiple putative metabolite quantitative trait loci (mQTL) which were validated through pedigree-based analyses. The research highlighted the importance of multiomic integration in advancing data-driven, phytochemical-based plant breeding.

NEW PHYTOLOGIST (2021)

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Review Biotechnology & Applied Microbiology

Current status of structural variation studies in plants

Yuxuan Yuan et al.

Summary: Structural variations (SVs) are common features in plant genomes and play important roles in the phenotypic diversity of plants. With the advancement of genomic technologies, we are now able to better understand and assess SVs with higher resolution. Plant breeders can leverage this research to improve varieties.

PLANT BIOTECHNOLOGY JOURNAL (2021)

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Article Plant Sciences

The application of pangenomics and machine learning in genomic selection in plants

Philipp E. Bayer et al.

Summary: Using state-of-the-art machine learning approaches to accelerate plant breeding and incorporating nonadditive effects in genomic selection can support crop improvement to counter the adverse outcomes of climate change on crop production.

PLANT GENOME (2021)

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Article Plant Sciences

Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain

Pradeep Ruperao et al.

Summary: The study constructed the sorghum pan-genome, revealing its structural and functional characteristics, and analyzing its role in genetic gain and drought adaptation. Results showed that the sorghum genome has rich gene diversity that can be utilized in crop improvement.

FRONTIERS IN PLANT SCIENCE (2021)

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Article Multidisciplinary Sciences

Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa

Guangpeng Ren et al.

Summary: The study reveals the domestication history of Cannabis sativa, indicating that it was first domesticated in early Neolithic times in East Asia, and that both hemp and drug cultivars diverged from an ancestral gene pool in China. Candidate genes associated with traits differentiating hemp and drug cultivars were identified, as well as evidence for loss of function of genes involved in cannabinoid synthesis during selection.

SCIENCE ADVANCES (2021)

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Article Plant Sciences

Representation and participation across 20 years of plant genome sequencing

Rose A. Marks et al.

Summary: In the past 20 years, the field of plant genome sequencing has grown rapidly, resulting in increased quantity and quality of publicly available genomic resources. However, significant taxonomic gaps exist, and the field has been primarily dominated by affluent nations in the Global North.

NATURE PLANTS (2021)

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Article Biotechnology & Applied Microbiology

Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

Wei Hu et al.

Summary: Heterozygous genomes are common in outcrossing and clonally propagated crops, with their variation underlying key agronomic traits and crop domestication largely unknown. A study on cassava reveals allelic variations in heterozygosity associated with agronomic traits and domestication, providing valuable insights for the improvement of cassava and other highly heterozygous crops.

GENOME BIOLOGY (2021)

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Article Biotechnology & Applied Microbiology

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

Feiyang Ji et al.

Summary: This study generated a comprehensive walnut genomic variation map based on whole-genome resequencing, revealing extensive hybridization between Chinese J. regia and J. sigillata, increasing genetic diversity and heterozygous mutations during improvement, and identifying major-effect loci involved in walnut adaptations and agronomic traits.

GENOME BIOLOGY (2021)

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Article Biotechnology & Applied Microbiology

Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice

Ning Xiao et al.

Summary: This study conducted large-scale genomic landscape analysis of japonica rice varieties grown in central China and identified several superior alleles related to yield, resistance to rice blast, and taste quality. By introducing these alleles into two high-yield cultivars, two elite lines, XY99 and JXY1, were successfully developed with excellent taste, high yield, and broad-spectrum of blast resistance, demonstrating a balancing of multiple agronomic traits through genomic-based strategy.

GENOME BIOLOGY (2021)

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Review Multidisciplinary Sciences

Genome-wide association studies

Emil Uffelmann et al.

Summary: Genome-wide association studies (GWAS) involve testing hundreds of thousands of genetic variants to identify those associated with specific traits or diseases, with the number of associated variants expected to increase as sample sizes grow. The results of GWAS have various applications, including understanding the underlying biology of phenotypes, estimating heritability, predicting clinical risks, guiding drug development programs, and inferring causal relationships between risk factors and health outcomes.

NATURE REVIEWS METHODS PRIMERS (2021)

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Article Biotechnology & Applied Microbiology

Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance

Xi Wu et al.

Summary: The study introduced a high-throughput multiple optical phenotyping system to phenotype 368 maize genotypes under drought stress. Through the analysis of image-based traits, it identified 10,080 effective and heritable indicators of maize drought responses, revealing numerous significant locus-trait associations and candidate genes. The combination of high-throughput phenotyping and GWAS proved to be an effective approach in dissecting the genetic architecture of complex traits and identifying genes associated with drought tolerance.

GENOME BIOLOGY (2021)

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Review Plant Sciences

Resources for image-based high-throughput phenotyping in crops and data sharing challenges

Monica F. Danilevicz et al.

Summary: High-throughput phenotyping platforms monitor plant phenotypic variation through various sensors and provide valuable resources for characterizing crop phenotypes. Researchers can utilize these datasets for phenotype comparison, benchmarking tool performance, and developing tools that generalize better across different crops and environments. Sharing phenotypic data is emphasized to assist crop breeders and tool developers in accelerating crop breeding.

PLANT PHYSIOLOGY (2021)

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Article Biotechnology & Applied Microbiology

Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits

Kaixuan Zhang et al.

Summary: This study reveals the domestication history of Tartary buckwheat and provides a comprehensive database of genomic variation, allowing for genomic-assisted breeding to enhance elite cultivars. The analysis indicates two independent domestication events in southwestern and northern China, leading to diverse characteristics in modern Tartary buckwheat varieties. Genome-wide association studies identified candidate genes related to flavonoid accumulation and grain weight, such as FtUFGT3 and FtAP2YT1.

GENOME BIOLOGY (2021)

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Article Agronomy

Identification and mapping of new genes for resistance to downy mildew in lettuce

Lorena Parra et al.

Summary: A study successfully introgressed eleven new major resistance genes for lettuce downy mildew from wild Lactuca species, mapping them to specific regions in the lettuce genome. This provides the foundation for marker-assisted selection to breed cultivars with multiple resistance genes for downy mildew.

THEORETICAL AND APPLIED GENETICS (2021)

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Article Plant Sciences

A role for the OsHKT 2;1 sodium transporter in potassium use efficiency in rice

Thomas N. Hartley et al.

JOURNAL OF EXPERIMENTAL BOTANY (2020)

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Article Biotechnology & Applied Microbiology

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