scholarly journals Development of an Australian Bread Wheat Nested Association Mapping Population, a New Genetic Diversity Resource for Breeding under Dry and Hot Climates

2021 ◽  
Vol 22 (9) ◽  
pp. 4348
Author(s):  
Charity Chidzanga ◽  
Delphine Fleury ◽  
Ute Baumann ◽  
Dan Mullan ◽  
Sayuri Watanabe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Mapping ◽  
Plant Height ◽  
Complex Traits ◽  
Snp Array ◽  
Genotyping By Sequencing ◽  
Nested Association Mapping ◽  
Modern Agriculture ◽  
Molecular Inversion Probes ◽  
Gwas Approach

Genetic diversity, knowledge of the genetic architecture of the traits of interest and efficient means of transferring the desired genetic diversity into the relevant genetic background are prerequisites for plant breeding. Exotic germplasm is a rich source of genetic diversity; however, they harbor undesirable traits that limit their suitability for modern agriculture. Nested association mapping (NAM) populations are valuable genetic resources that enable incorporation of genetic diversity, dissection of complex traits and providing germplasm to breeding programs. We developed the OzNAM by crossing and backcrossing 73 diverse exotic parents to two Australian elite varieties Gladius and Scout. The NAM parents were genotyped using the iSelect wheat 90K Infinium SNP array, and the progeny were genotyped using a custom targeted genotyping-by-sequencing assay based on molecular inversion probes designed to target 12,179 SNPs chosen from the iSelect wheat 90K Infinium SNP array of the parents. In total, 3535 BC1F4:6 RILs from 125 families with 21 to 76 lines per family were genotyped and we found 4964 polymorphic and multi-allelic haplotype markers that spanned the whole genome. A subset of 530 lines from 28 families were evaluated in multi-environment trials over three years. To demonstrate the utility of the population in QTL mapping, we chose to map QTL for maturity and plant height using the RTM-GWAS approach and we identified novel and known QTL for maturity and plant height.

scholarly journals Genotyping-by-Sequencing-Based Genetic Analysis of African Rice Cultivars and Association Mapping of Blast Resistance Genes Against Magnaporthe oryzae Populations in Africa

2017 ◽  
Vol 107 (9) ◽  
pp. 1039-1046 ◽  
Author(s):  
Emmanuel M. Mgonja ◽  
Chan Ho Park ◽  
Houxiang Kang ◽  
Elias G. Balimponya ◽  
Stephen Opiyo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Mapping ◽  
Magnaporthe Oryzae ◽  
Rice Blast ◽  
Blast Resistance ◽  
Genotyping By Sequencing ◽  
Rice Breeding ◽  
Rice Cultivars ◽  
R Genes ◽  
African Rice

Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs). The 190 African cultivars were clustered into three groups based on the 184K single nucleotide polymorphisms generated by GBS. We inoculated the rice cultivars with six African M. oryzae isolates. Association mapping identified 25 genomic regions associated with blast resistance (RABRs) in the rice genome. Moreover, PCR analysis indicated that RABR_23 is associated with the Pi-ta gene on chromosome 12. Our study demonstrates that the combination of GBS-based genetic diversity population analysis and association mapping is effective in identifying rice blast R genes/QTLs that contribute to resistance against African populations of M. oryzae. The identified markers linked to the RABRs and 14 highly resistant cultivars in this study will be useful for rice breeding in Africa.

scholarly journals Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0155760 ◽  
Author(s):  
Prabin Bajgain ◽  
Matthew N. Rouse ◽  
Toi J. Tsilo ◽  
Godwin K. Macharia ◽  
Sridhar Bhavani ◽  
...  
Keyword(s):  
Association Mapping ◽  
Stem Rust ◽  
Rust Resistance ◽  
Genotyping By Sequencing ◽  
Stem Rust Resistance ◽  
Nested Association Mapping

scholarly journals TeoNAM: a nested association mapping population for domestication and agronomic trait analysis in maize

2019 ◽  
Author(s):  
Qiuyue Chen ◽  
Chin Jian Yang ◽  
Alessandra M. York ◽  
Wei Xue ◽  
Lora L. Daskalska ◽  
...  
Keyword(s):  
Association Mapping ◽  
Complex Traits ◽  
Agronomic Traits ◽  
Mapping Population ◽  
Allelic Variation ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Nested Association Mapping ◽  
Nested Association Mapping Population ◽  
Association Mapping Population

AbstractRecombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping population (TeoNAM), derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTLs from JLM were identified with many of these mapping to known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTLs for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.

scholarly journals Identification of marker-trait associated SNPs for fruit weight and plant height in a wild and domesticated jujube fruit tree (Ziziphus spp.) collection using genotyping-by-sequencing

2021 ◽  
Author(s):  
Nisar Uddin ◽  
Harshraj Shinde ◽  
Kiflu Tesfamicael ◽  
Niaz Ali ◽  
Penny J Tricker ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Height ◽  
Genome Wide Association Study ◽  
Polymorphic Information Content ◽  
Genotyping By Sequencing ◽  
Fruit Weight ◽  
Ziziphus Mauritiana ◽  
Principal Coordinates ◽  
A Genome ◽  
Jujube Fruit

Ziziphus are economically and nutritionally important fruiting plants that were domesticated in China around 7000 years ago. We identified genetic diversity in 141 accessions of four, different species collected in Pakistan and in China, including wild species of Ziziphus mauritiana, Z. nummularia and Z. oxyphllya, and both wild and domesticated Z. jujuba Mill. Population structure, phylogenetic analysis and principal coordinates analysis based on 10,889 high-quality SNPs derived from genotyping-by-sequencing indicated that the accessions clustered into two major groups. The wild Pakistani Z. jujuba and Z. nummularia exhibited higher genetic diversity and polymorphic information content (0.37 and 0.23 respectively) than other species. We further conducted a genome-wide association study and discovered six highly significant marker-trait associations for fruit weight and plant height in this population. Our study provides important information for future breeding of Ziziphus species.

scholarly journals A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies

PLoS Genetics ◽  
2012 ◽  
Vol 8 (1) ◽  
pp. e1002451 ◽  
Author(s):  
Molly E. McCue ◽  
Danika L. Bannasch ◽  
Jessica L. Petersen ◽  
Jessica Gurr ◽  
Ernie Bailey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Mapping ◽  
Snp Array ◽  
High Density ◽  
Domestic Horse

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 A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations

2021 ◽  
Vol 11 ◽  
Author(s):  
Suhong Bu ◽  
Weiren Wu ◽  
Yuan-Ming Zhang
Keyword(s):  
Association Mapping ◽  
Linkage Mapping ◽  
Complex Traits ◽  
Association Studies ◽  
New Method ◽  
Genome Wide Association Studies ◽  
Single Family ◽  
Association Model ◽  
Model Framework ◽  
Nested Association Mapping

Nested association mapping (NAM) has been an invaluable approach for plant genetics community and can dissect the genetic architecture of complex traits. As the most popular NAM analysis strategy, joint multifamily mapping can combine all information from diverse genetic backgrounds and increase population size. However, it is influenced by the genetic heterogeneity of quantitative trait locus (QTL) across various subpopulations. Multi-locus association mapping has been proven to be powerful in many cases of QTL mapping and genome-wide association studies. Therefore, we developed a multi-locus association model of multiple families in the NAM population, which could discriminate the effects of QTLs in all subpopulations. A series of simulations with a real maize NAM genomic data were implemented. The results demonstrated that the new method improves the statistical power in QTL detection and the accuracy in QTL effect estimation. The new approach, along with single-family linkage mapping, was used to identify QTLs for three flowering time traits in the maize NAM population. As a result, most QTLs detected in single family linkage mapping were identified by the new method. In addition, the new method also mapped some new QTLs with small effects, although their functions need to be identified in the future.

scholarly journals Genetic Diversity of Purple Passion Fruit, Passiflora edulis f. edulis, Based on Single-Nucleotide Polymorphism Markers Discovered through Genotyping by Sequencing

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 144
Author(s):  
Nohra Castillo Rodríguez ◽  
Xingbo Wu ◽  
María Isabel Chacón ◽  
Luz Marina Melgarejo ◽  
Matthew Wohlgemuth Blair
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genotyping By Sequencing ◽  
Passion Fruit ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Passiflora Edulis ◽  
Tropical Fruit ◽  
Commercial Cultivars ◽  
Purple Passion Fruit

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

scholarly journals Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 10
Author(s):  
Sebastian Zahn ◽  
Thomas Schmutzer ◽  
Klaus Pillen ◽  
Andreas Maurer
Keyword(s):  
Quantitative Trait Loci ◽  
Association Mapping ◽  
Cross Section ◽  
Quantitative Trait ◽  
Spring Barley ◽  
Raw Material ◽  
Total Thickness ◽  
Nested Association Mapping ◽  
Elite Cultivar ◽  
Major Qtl

Straw biomass and stability are crucial for stable yields. Moreover, straw harbors the potential to serve as a valuable raw material for bio-economic processes. The peduncle is the top part of the last shoot internode and carries the spike. This study investigates the genetic control of barley peduncle morphology. Therefore, 1411 BC1S3 lines of the nested association mapping (NAM) population “Halle Exotic Barley 25” (HEB-25), generated by crossing the spring barley elite cultivar Barke with an assortment of 25 exotic barley accessions, were used. Applying 50k Illumina Infinium iSelect SNP genotyping yielded new insights and a better understanding of the quantitative trait loci (QTL) involved in controlling the peduncle diameter traits, we found the total thickness of peduncle tissues and the area of the peduncle cross-section. We identified three major QTL regions on chromosomes 2H and 3H mainly impacting the traits. Remarkably, the exotic allele at the QTL on chromosome 3H improved all three traits investigated in this work. Introgressing this QTL in elite cultivars might facilitate to adjust peduncle morphology for improved plant stability or enlarged straw biomass production independent of flowering time and without detrimental effects on grain yield.

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