scholarly journals Identification of candidate genes responsible for morphological and yield-related traits via genome-wide association analysis (GWAS) in oil palm (Elaeis oleifera x Elaeis guineensis)

2019 ◽  
Author(s):  
Jaime Osorio ◽  
Gina Garzón ◽  
Paola Delgadillo ◽  
Silvio Bastidas ◽  
Leidy Moreno ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Oil Palm ◽  
Plant Architecture ◽  
Elaeis Guineensis ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Hybrid Population ◽  
Elaeis Oleifera ◽  
Genome Wide

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. The breeding program in Colombia relies on interspecific OxG crossing populations with tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. The identification of loci associated to morphological and yield-related traits and the dissection of their genetic architecture will provide essential insights for oil palm breeding strategies. Results The genotypes of 471 oil palms, including 62 E. oleifera (O), 31 E. guineensis (G) and 378 OxG samples were analyzed in this study. A total of 3,776 single nucleotide polymorphisms (SNP) were detected across the 16 oil palm chromosomes using the genotyping-by-sequencing (GBS) technique. The genetic variation and population structure analyses grouped the samples into two clades according to the parental relatedness. A genome wide association analysis (GWAS) was conducting using the OxG hybrid population, resulting in 12 SNPs significantly associated with ten different morphological and yield-related traits. Conclusions The work presented herein provides to our knowledge the first association mapping study in an interspecific OxG hybrid population of oil palm. We provide new insights on candidate genes involved in tissue development and plant architecture associated to traits such as: rachis length, trunk diameter, bunch number, and bunch weight. The genes identified in our analysis are putative candidates for future targeted functional analysis. They are valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis, Elaeis oleifera, genotyping-by-sequencing, plant architecture, yield.

scholarly journals Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

2019 ◽  
Author(s):  
Jaime Osorio ◽  
Gina Garzón ◽  
Paola Delgadillo ◽  
Silvio Bastidas ◽  
Leidy Moreno ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Oil Palm ◽  
Plant Architecture ◽  
Elaeis Guineensis ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis , Elaeis oleifera , genotyping-by-sequencing, plant architecture, yield.

scholarly journals Genome wide association study (GWAS) for morphological and yield-related traits in oil palm hybrids (Elaeis oleifera x Elaeis guineensis)

2019 ◽  
Author(s):  
Jaime Osorio ◽  
Gina Garzón ◽  
Paola Delgadillo ◽  
Silvio Bastidas ◽  
Leidy Moreno ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Oil Palm ◽  
Plant Architecture ◽  
Elaeis Guineensis ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
Genomic Regions

Abstract Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. The work presented herein provides, to our knowledge, the first association mapping study in an interspecific OxG hybrid population of oil palm which presents tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrids for 10 agronomic traits. Twelve genomic regions were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on candidate genes that mapped on genomic regions involved in plant architecture and yield; however, these potential candidate genes need to be confirmed for future targeted functional analysis. The associated markers may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis, Elaeis oleifera, genotyping-by-sequencing, plant architecture, yield.

scholarly journals Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

2019 ◽  
Author(s):  
Jaime Osorio ◽  
Gina Garzón ◽  
Paola Delgadillo ◽  
Silvio Bastidas ◽  
Leidy Moreno ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Oil Palm ◽  
Plant Architecture ◽  
Elaeis Guineensis ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis , Elaeis oleifera , genotyping-by-sequencing, plant architecture, yield.

scholarly journals Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Gina A. Garzón-Martínez ◽  
Paola Delgadillo-Duran ◽  
Silvio Bastidas ◽  
Leidy P. Moreno ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Genome Wide Association ◽  
Hybrid Population ◽  
Potential Candidate ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding.

scholarly journals Genome-Wide Association Study (GWAS) for Bunch Components of The Interspecific Population of Elaeis oleifera and Elaeis guineensis

2021 ◽  
Vol 29 (2) ◽  
pp. 97-114
Author(s):  
Heri Adriwan Siregar ◽  
Edy Suprianto ◽  
Sujadi Sujadi ◽  
Hernawan Y Rahmadi ◽  
Mohamad Arif ◽  
...  
Keyword(s):  
Oil Palm ◽  
Genome Wide Association Study ◽  
Elaeis Guineensis ◽  
Genotyping By Sequencing ◽  
Breeding Program ◽  
Phenotypic Data ◽  
Single Nucleotide ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
Alternative Approach

The oil palm breeding program for the species Elaeis guineensis and the backcross Elaeis oleifera is running slowly because oil palm is an annual plant. Therefore, it is necessary to have an alternative approach that can accelerate the oil palm breeding program. The SNP (single nucleotide polymorphism) genome-wide approach was then used to study the association between 18 phenotypes of bunch component in oil palm germplasm of E. oleifera from Suriname and Brazil Coari, some interspecific hybrids and some elite progeny of E. guineensis. The genotyping by sequencing (GBS) analysis produced a total of 459 million or approximately 798 thousand reads per sample and 3,252 SNPs were eligible for 456 genotypes. Using various association models, eleven normalized phenotypic data showed significant associations with 29 SNPs. Based on the annotations, 17 SNPs were related to genes wtih certain biological functions. Three SNPs were found to be at the exon of a gene, namely SNP4416, SNP349 and SNP3865, while the other 15 SNPs were at the intragenic to a gene. Four SNPs are common SNPs in phenotypes C16:0 and C18:1 as weel as in C20 0 and C20:1. This research shows the potential of SNPs that can be used as an alternative approach to E. oleifera backcross breeding, although further research is needed for validation purposes.

scholarly journals Genome-Wide Association Mapping for Heat and Drought Adaptive Traits in Pea

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1897
Author(s):  
Endale G. Tafesse ◽  
Krishna K. Gali ◽  
V. B. Reddy Lachagari ◽  
Rosalind Bueckert ◽  
Thomas D. Warkentin
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Vegetation Index ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Adaptive Traits ◽  
Flowering Duration ◽  
Genome Wide ◽  
A Genome

Heat and drought, individually or in combination, limit pea productivity. Fortunately, substantial genetic diversity exists in pea germplasm for traits related to abiotic stress resistance. Understanding the genetic basis of resistance could accelerate the development of stress-adaptive cultivars. We conducted a genome-wide association study (GWAS) in pea on six stress-adaptive traits with the aim to detect the genetic regions controlling these traits. One hundred and thirty-five genetically diverse pea accessions were phenotyped in field studies across three or five environments under stress and control conditions. To determine marker trait associations (MTAs), a total of 16,877 valuable single nucleotide polymorphisms (SNPs) were used in association analysis. Association mapping detected 15 MTAs that were significantly (p ≤ 0.0005) associated with the six stress-adaptive traits averaged across all environments and consistent in multiple individual environments. The identified MTAs were four for lamina wax, three for petiole wax, three for stem thickness, two for the flowering duration, one for the normalized difference vegetation index (NDVI), and two for the normalized pigment and chlorophyll index (NPCI). Sixteen candidate genes were identified within a 15 kb distance from either side of the markers. The detected MTAs and candidate genes have prospective use towards selecting stress-hardy pea cultivars in marker-assisted selection.

scholarly journals Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat

2020 ◽  
Vol 21 (2) ◽  
pp. 394 ◽  
Author(s):  
Daniela Marone ◽  
Monica Rodriguez ◽  
Sergio Saia ◽  
Roberto Papa ◽  
Domenico Rau ◽  
...  
Keyword(s):  
Plant Growth ◽  
Association Mapping ◽  
Durum Wheat ◽  
Candidate Genes ◽  
Zinc Finger ◽  
Growth Habit ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Plant Growth Habit ◽  
Tiller Angle

By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.

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