4.7 Article

Genome-wide artificial introgressions of Gossypium barbadense into G. hirsutum reveal superior loci for simultaneous improvement of cotton fiber quality and yield traits

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biotechnology & Applied Microbiology

Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance

Nan Zhao et al.

Summary: The study identified key genes affecting fiber quality, yield, and disease resistance in Sea Island cotton through genome-wide association study, and discovered two major gene pools and a mixed subgroup. Pedigree selection breeding improved fiber quality, yield, and Fusarium wilt disease resistance in Sea Island cotton.

PLANT BIOTECHNOLOGY JOURNAL (2022)

Article Plant Sciences

Introgression from Gossypium hirsutum is a driver for population divergence and genetic diversity in Gossypium barbadense

Pengpeng Wang et al.

Summary: This study reveals the genetic basis of population differentiation and genetic diversity in Gossypium barbadense, as well as introgression events and haplotype selection affecting fiber quality and environmental adaptation.

PLANT JOURNAL (2022)

Article Biotechnology & Applied Microbiology

Divergent improvement of two cultivated allotetraploid cotton species

Lei Fang et al.

Summary: Interspecific genomic variation plays a crucial role in local adaptation and domestication. Studies on two allotetraploid Gossypium species, G. barbadense and G. hirsutum, revealed divergent improvement between the species and identified interspecific introgressions significantly associated with agronomic traits. The findings suggest the potential value of interspecific introgressions in hybridization and precision breeding for further improvements in yield and fiber qualities.

PLANT BIOTECHNOLOGY JOURNAL (2021)

Editorial Material Genetics & Heredity

Quantitative genetics: pan-genomes, SVs, and k-mers for GWAS

Pushpendra K. Gupta

Summary: Over the past two decades, thousands of genome-wide association studies have been conducted to identify marker-trait associations for complex traits in animals and plants, involving continuous improvement in methodology. Initially, a reference genome and SNPs were used, but more recently pan-genomes and markers structural variations (SVs)/k-mers are also being utilized.

TRENDS IN GENETICS (2021)

Article Plant Sciences

Identification of Candidate Cotton Genes Associated With Fiber Length Through Quantitative Trait Loci Mapping and RNA-Sequencing Using a Chromosome Segment Substitution Line

Quanwei Lu et al.

Summary: Fiber length is a crucial determinant of fiber quality and a quantitative multi-genic trait. This study identified QTLs associated with fiber length and strength on four chromosomes, as well as promising candidate genes through transcriptomic data integration and qPCR analyses. Establishing populations and confirming QTLs in multiple environments provide a solid foundation for further research on the molecular basis of fiber length and efforts to improve cotton fiber quality.

FRONTIERS IN PLANT SCIENCE (2021)

Article Genetics & Heredity

The genomic basis of geographic differentiation and fiber improvement in cultivated cotton

Shoupu He et al.

Summary: The study revealed that extensive chromosome inversions on chromosomes A06 and A08 underlies the geographic differentiation in cultivated cotton, and haplotypic diversity from landraces is essential for adaptive evolution. Introgression and association analyses identified new fiber quality-related loci, showing that introgressed alleles from diploid cottons have a large effect on fiber quality improvement.

NATURE GENETICS (2021)

Article Chemistry, Multidisciplinary

Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton

Daojun Yuan et al.

Summary: Two cultivated allopolyploid cottons, G. hirsutum and G. barbadense, underwent parallel independent domestication processes, involving significant morphological transformations. Wild forms of both species were initially domesticated in the Yucatan Peninsula and NW South America, respectively, before spreading over 4000-8000 years to encompass most of the American tropics. Genome-wide bidirectional introgression occurred between the two co-resident genomes of these allopolyploids, revealing genetic asymmetries and regions targeted during domestication.

ADVANCED SCIENCE (2021)

Article Biochemistry & Molecular Biology

GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers

Pushpendra K. Gupta

Summary: The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research in the past 25 years. With the availability of high throughput next generation sequencing (NGS) technology, the use of pangenomes and novel markers for GWAS has taken over as a new thrust area of research.

BIOESSAYS (2021)

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)

Article Plant Sciences

Reciprocal allopolyploid grasses (Festuca x Lolium) display stable patterns of genome dominance

Marek Glombik et al.

Summary: Allopolyploidization, involving the merger of two distinct genomes, is essential in plant evolution and breeding programs. Research on Festuca pratensis Huds. x Lolium multiflorum Lam. grasses found that the dominance of Lolium genome in gene expression is heritable and minimally affected by environmental conditions and plant age. This dominance may be partly attributed to more efficient trans-acting gene expression regulatory factors in Lolium.

PLANT JOURNAL (2021)

Article Agronomy

Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage

Jingwen Yu et al.

Summary: Genetic variation in a G. barbadense population was revealed through resequencing, identifying candidate genes associated with fiber quality. GWAS confirmed associations between several traits and specific genes, highlighting potential targets for genetic engineering in G. barbadense breeding.

THEORETICAL AND APPLIED GENETICS (2021)

Article Biochemical Research Methods

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files

Shan-Shan Dong et al.

Summary: LDBlockShow is an open source software that visualizes LD and haplotype blocks, providing faster speed and lower memory consumption compared to other tools.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biotechnology & Applied Microbiology

The genetic mechanism of heterosis utilization in maize improvement

Yingjie Xiao et al.

Summary: The study demonstrates that although yield heterosis in maize hybrids is correlated with minor-effect epistatic QTLs, it may be the result of major-effect additive and dominant QTLs during early developmental stages. The transition to flowering is identified as a critical stage for heterosis formation, where epistatic QTLs are activated by paternal alleles counteracting deleterious maternal alleles. The proposed molecular breeding approach targets key genes to accelerate maize breeding by reducing deleterious epistatic interactions.

GENOME BIOLOGY (2021)

Article Biotechnology & Applied Microbiology

Cotton pan-genome retrieves the lost sequences and genes during domestication and selection

Jianying Li et al.

Summary: The research constructed a comprehensive genomic variome, identified loci associated with domestication and improvement selection signals, and analyzed genes related to agronomic traits. Additionally, pan-genome analysis revealed a large number of non-reference genes lost from the reference genomes, and showed the presence/absence variation, indicating genetic diversity changes driven by locus selection.

GENOME BIOLOGY (2021)

Article Biotechnology & Applied Microbiology

Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

Zegang Han et al.

PLANT BIOTECHNOLOGY JOURNAL (2020)

Article Genetics & Heredity

The Causes and Consequences of Genetic Interactions (Epistasis)

Júlia Domingo et al.

Annual Review of Genomics and Human Genetics (2019)

Review Biotechnology & Applied Microbiology

Breeding crops to feed 10 billion

Lee T. Hickey et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

QTL Mapping for Fiber Quality and Yield Traits Based on Introgression Lines Derived from Gossypium hirsutum x G-tomentosum

Ayaz Ali Keerio et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2018)

Article Multidisciplinary Sciences

The complex underpinnings of genetic background effects

Martin N. Mullis et al.

NATURE COMMUNICATIONS (2018)

Article Biotechnology & Applied Microbiology

Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.

Zhengwen Sun et al.

PLANT BIOTECHNOLOGY JOURNAL (2017)

Article Biotechnology & Applied Microbiology

Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

Lei Fang et al.

GENOME BIOLOGY (2017)

Editorial Material Genetics & Heredity

Bringing genetic background into focus

Clement Y. Chow

NATURE REVIEWS GENETICS (2016)

Article Agriculture, Multidisciplinary

Heterotic loci identified for plant height and ear height using two CSSLs test populations in maize

Wang Hong-qiu et al.

JOURNAL OF INTEGRATIVE AGRICULTURE (2016)

Article Biochemistry & Molecular Biology

Development, identification and utilization of introgression lines using Chinese endemic and synthetic wheat as donors

Liqing Gu et al.

JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2015)

Article Biotechnology & Applied Microbiology

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Tianzhen Zhang et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemistry & Molecular Biology

Constructing a high-density linkage map for Gossypium hirsutum x Gossypium barbadense and identifying QTLs for lint percentage

Yuzhen Shi et al.

JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2015)

Article Biochemistry & Molecular Biology

A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum x G. barbadense populations

Joseph I. Said et al.

MOLECULAR GENETICS AND GENOMICS (2015)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Genetics & Heredity

De novo assembly and genotyping of variants using colored de Bruijn graphs

Zamin Iqbal et al.

NATURE GENETICS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Genetics & Heredity

A modified algorithm for the improvement of composite interval mapping

Huihui Li et al.

GENETICS (2007)

Article Biochemical Research Methods

R/qtl: QTL mapping in experimental crosses

KW Broman et al.

BIOINFORMATICS (2003)