scholarly journals Association Mapping for Improving Fiber Quality in Upland Cottons

2021 ◽  
Author(s):  
Khezir Hayat ◽  
Adem Bardak ◽  
Mehboob-ur-Rahman ◽  
Hafiz Muhammad Imran ◽  
Furqan Ahmad ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Association Mapping ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Fiber Quality ◽  
Crop Species ◽  
Genomic Tools ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Mapping Populations

Improved fiber yield is considered a constant goal of upland cotton (Gossypium hirsutum) breeding worldwide, but the understanding of the genetic basis controlling yield-related traits remains limited. Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists. Two complementary approaches for genetic mapping, linkage mapping and association mapping have led to successful dissection of complex traits in many crop species. Both of these methods detect quantitative trait loci (QTL) by identifying marker–trait associations, and the only fundamental difference between them is that between mapping populations, which directly determine mapping resolution and power. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information with the development of high-throughput genotyping, phenotyping will be a major challenge for genetic mapping studies. We believe that high-quality phenotyping and appropriate experimental design coupled with new statistical models will accelerate progress in dissecting the genetic architecture of complex traits.

scholarly journals The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp. parviglumis): New Evidence From Association Mapping

Genetics ◽  
2008 ◽  
Vol 180 (2) ◽  
pp. 1221-1232 ◽  
Author(s):  
Allison L. Weber ◽  
William H. Briggs ◽  
Jesse Rucker ◽  
Baltazar M. Baltazar ◽  
José de Jesús Sánchez-Gonzalez ◽  
...  
Keyword(s):  
Zea Mays ◽  
Association Mapping ◽  
Complex Traits ◽  
Genetic Architecture ◽  
New Evidence

scholarly journals Evolutionary insights into plant breeding

2019 ◽  
Author(s):  
Sarah Diane Turner-Hissong ◽  
Makenzie E. Mabry ◽  
Timothy M. Beissinger ◽  
Jeffrey Ross-Ibarra ◽  
J. Chris Pires
Keyword(s):  
Plant Breeding ◽  
Complex Traits ◽  
Life Histories ◽  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Demographic History ◽  
Crop Improvement ◽  
Community Resources ◽  
Crop Species ◽  
Selection Strategies

Crop domestication is a fascinating area of study, as evidenced by a multitude of recent reviews. Coupled with the increasing availability of genomic and phenomic resources in numerous crop species, insights from evolutionary biology will enable a deeper understanding of the genetic architecture and short-term evolution of complex traits, which can be used to inform selection strategies. Future advances in crop improvement will rely on the integration of population genetics with plant breeding methodology, and the development of community resources to support research in a variety of crop life histories and reproductive strategies. We highlight recent advances in the role of selective sweeps and demographic history in shaping genetic architecture, how these breakthroughs can inform selection strategies, and the application of precision gene editing to leverage these connections.

scholarly journals Application of Association Mapping to Understanding the Genetic Diversity of Plant Germplasm Resources

2008 ◽  
Vol 2008 ◽  
pp. 1-18 ◽  
Author(s):  
Ibrokhim Y. Abdurakhmonov ◽  
Abdusattor Abdukarimov
Keyword(s):  
Association Mapping ◽  
Complex Traits ◽  
Plant Genomics ◽  
Crop Breeding ◽  
Crop Species ◽  
Simple Description ◽  
Mapping Tool ◽  
High Resolution Mapping ◽  
Resolution Mapping ◽  
International Plant

Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a “powerful gene tagging” tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application.

scholarly journals Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Heredity ◽  
2020 ◽  
Vol 125 (6) ◽  
pp. 396-416 ◽  
Author(s):  
Michael F. Scott ◽  
Olufunmilayo Ladejobi ◽  
Samer Amer ◽  
Alison R. Bentley ◽  
Jay Biernaskie ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genetic Mapping ◽  
Quantitative Trait ◽  
Complex Traits ◽  
De Novo ◽  
Sequence Information ◽  
Genetic Dissection ◽  
Crop Species ◽  
High Genetic Diversity ◽  
Trait Loci

Abstract Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm ‘package’ that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.

scholarly journals Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass

2021 ◽  
Author(s):  
Kayla R Altendorf ◽  
Steve Larson ◽  
Lee R DeHaan ◽  
Jared Crain ◽  
Jeff Neyhart ◽  
...  
Keyword(s):  
Association Mapping ◽  
Flowering Time ◽  
Genetic Control ◽  
Genetic Architecture ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Grass Species ◽  
Crop Species ◽  
Nested Association Mapping ◽  
Intermediate Wheatgrass

Abstract Intermediate wheatgrass (Thinopyrum intermedium) is an outcrossing, cool season grass species currently undergoing direct domestication as a perennial grain crop. Though many traits are selection targets, understanding the genetic architecture of those important for local adaptation may accelerate the domestication process. Nested association mapping (NAM) has proven useful in dissecting the genetic control of agronomic traits many crop species, but its utility in primarily outcrossing, perennial species has yet to be demonstrated. Here we introduce an intermediate wheatgrass NAM developed by crossing ten phenotypically divergent donor parents to an adapted common parent in a reciprocal manner, yielding 1,168 F1 progeny from 10 families. Using genotyping by sequencing, we identified 8,003 SNP markers and developed a population-specific consensus genetic map with 3,144 markers across 21 linkage groups. Using both genomewide association mapping and linkage mapping combined across and within families, we characterize the genetic control of flowering time. In the analysis of two measures of maturity across four separate environments, we detected as many as 75 significant QTL, many of which correspond to the same regions in both analysis methods across 11 chromosomes. The results demonstrate a complex genetic control that is variable across years, locations, traits, and within families. The methods were effective at detecting previously identified QTL, as well as new QTL that align closely to the well-characterized flowering time orthologs from barley, including Ppd-H1 and Constans. Our results demonstrate the utility of the NAM for understanding the genetic control of flowering time and its potential for application to other traits of interest.

scholarly journals Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant

2018 ◽  
Vol 46 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Pietro GRAMAZIO ◽  
Jaime PROHENS ◽  
Mariola PLAZAS ◽  
Giulio MANGINO ◽  
Francisco J. HERRAIZ ◽  
...  
Keyword(s):  
Solanum Melongena ◽  
Relevant Information ◽  
Wild Relatives ◽  
Biological Processes ◽  
Vegetable Crops ◽  
Genomic Tools ◽  
Wide Range ◽  
Different Types ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Dramatic advances in genomics during the last decades have led to a revolution in the field of vegetable crops breeding. Some vegetables, like tomato, have served as model crops in the application of genomic tools to plant breeding but other important crops, like eggplant (Solanum melongena), lagged behind. The advent of next generation sequencing (NGS) technologies and the continuous decrease of the sequencing costs have allowed to develop genomic tools with a greatly benefit for no-model plants such as eggplant. In this review we present the currently available genomic resources in eggplant and discuss their interest for breeding. The first draft of eggplant genome sequence and the new upcoming improved assembly, as well as, the transcriptomes and RNA-based studies represent important genomic tools. The transcriptomes of cultivated eggplant and several wild relatives of eggplant are also available and have provided relevant information for the development of markers and understanding biological processes in eggplant. In addition, a historical overview of the eggplant genetic mapping studies, performed with different types of markers and experimental populations, provides a picture of the increase over time of the precision and resolution in the identification of candidate genes and QTLs for a wide range of stresses, and morpho-agronomic and domestication traits. Finally, we discuss how the development of new genetic and genomic tools in eggplant can pave the way for increasing the efficiency of eggplant breeding for developing improved varieties able to cope with the old and new challenges in horticultural production.

scholarly journals A Nested Association Mapping Panel in Arabidopsis thaliana for Mapping and Characterizing Genetic Architecture

2020 ◽  
Vol 10 (10) ◽  
pp. 3701-3708 ◽  
Author(s):  
Marcus T. Brock ◽  
Matthew J. Rubin ◽  
Dean DellaPenna ◽  
Cynthia Weinig
Keyword(s):  
Arabidopsis Thaliana ◽  
Association Mapping ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Recurrent Parent ◽  
Linkage Maps ◽  
Nucleotide Polymorphisms ◽  
Nested Association Mapping ◽  
Mapping Panel ◽  
Genotype By Sequencing

Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred line populations (RILs) of Arabidopsis thaliana, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate that our GBS markers have improved power to detect small effect QTL and enhanced resolution of QTL support intervals in comparison to original linkage maps. Using these robust linkage maps, we imputed a common set of publicly available parental SNPs into each RIL linkage map, generating overlapping markers across all populations. Though ultimately depending on allele frequencies at causal loci, simulations of the NAM panel suggest that surveying between 4 to 7 of the 14 RIL populations provides high resolution of the genetic architecture of complex traits, relative to a single mapping population.

scholarly journals Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

2011 ◽  
Vol 2 (1) ◽  
Author(s):  
Keyan Zhao ◽  
Chih-Wei Tung ◽  
Georgia C. Eizenga ◽  
Mark H. Wright ◽  
M. Liakat Ali ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Mapping ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Genome Wide Association ◽  
Genome Wide
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