scholarly journals Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1709
Author(s):  
Jae-Sung Lee ◽  
Dmytro Chebotarov ◽  
Kenneth L. McNally ◽  
Valerien Pede ◽  
Tri Deri Setiyono ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Gene Networks ◽  
A Priori ◽  
Resistance Mechanism ◽  
Economic Loss ◽  
Maturity Stage ◽  
Japonica Rice ◽  
Nucleotide Polymorphisms ◽  
A Genome ◽  
Rice Improvement

Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8–10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

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 Haplotypes within tandemly duplicated candidate genes at BnaA9.MRP5 modulate phytate concentration in canola (Brassica napus L.)

2021 ◽  
Author(s):  
Haijiang Liu ◽  
xiaojuan Li ◽  
Qianwen Zhang ◽  
pan yuan ◽  
Lei Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oilseed Rape ◽  
Genome Wide Association Study ◽  
Mineral Elements ◽  
Nucleotide Polymorphisms ◽  
Brassica Napus L ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Phytate Content

Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape B. napus (oilseed rape). Here, a panel of 505 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 x 106 single nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low -phytate variety (LPA20) was significantly elevated compared with a high -phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favorable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.

scholarly journals GWAS Discovery Of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 803 ◽  
Author(s):  
Wang ◽  
Yan ◽  
Li ◽  
Li ◽  
Zhao ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Market Demand ◽  
Oil Crops ◽  
A Genome ◽  
Genomic Regions

Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

scholarly journals Mapping of Diabetes Susceptibility Loci in a Domestic Cat Breed with an Unusually High Incidence of Diabetes Mellitus

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1369 ◽  
Author(s):  
Lois Balmer ◽  
Caroline Ann O’Leary ◽  
Marilyn Menotti-Raymond ◽  
Victor David ◽  
Stephen O’Brien ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Candidate Genes ◽  
The United States ◽  
Domestic Cat ◽  
Nucleotide Polymorphisms ◽  
Breeding Programs ◽  
Preventative Health ◽  
Genome Wide ◽  
A Genome

Genetic variants that are associated with susceptibility to type 2 diabetes (T2D) are important for identification of individuals at risk and can provide insights into the molecular basis of disease. Analysis of T2D in domestic animals provides both the opportunity to improve veterinary management and breeding programs as well as to identify novel T2D risk genes. Australian-bred Burmese (ABB) cats have a 4-fold increased incidence of type 2 diabetes (T2D) compared to Burmese cats bred in the United States. This is likely attributable to a genetic founder effect. We investigated this by performing a genome-wide association scan on ABB cats. Four SNPs were associated with the ABB T2D phenotype with p values <0.005. All exons and splice junctions of candidate genes near significant single-nucleotide polymorphisms (SNPs) were sequenced, including the genes DGKG, IFG2BP2, SLC8A1, E2F6, ETV5, TRA2B and LIPH. Six candidate polymorphisms were followed up in a larger cohort of ABB cats with or without T2D and also in Burmese cats bred in America, which exhibit low T2D incidence. The original SNPs were confirmed in this cohort as associated with the T2D phenotype, although no novel coding SNPs in any of the seven candidate genes showed association with T2D. The identification of genetic markers associated with T2D susceptibility in ABB cats will enable preventative health strategies and guide breeding programs to reduce the prevalence of T2D in these cats.

scholarly journals Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

2021 ◽  
Vol 12 ◽  
Author(s):  
Kelechi Uchendu ◽  
Damian Ndubuisi Njoku ◽  
Agre Paterne ◽  
Ismail Yusuf Rabbi ◽  
Daniel Dzidzienyo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome ◽  
Breeding Programmes ◽  
Vegetables And Fruits ◽  
Genomic Regions

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

scholarly journals Genome-wide Association Study and Possible Candidate Genes for Root Color and Carotenoid Contents in Japanese Orange Carrot F2 Populations

2021 ◽  
Author(s):  
Taeko Shibaya ◽  
Chika Kuroda ◽  
Hisano Tsuruoka ◽  
Chiharu Minami ◽  
Akiko Obara ◽  
...  
Keyword(s):  
Amino Acid ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Carotenoid Biosynthesis ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Visual Evaluation ◽  
Genome Wide ◽  
A Genome

Abstract Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed a genome-wide association study (GWAS) using genome-wide single-nucleotide polymorphisms (SNPs) in two F2 populations, both derived from crosses of orange root carrots bred by a Japanese seed company. The GWAS revealed 21 significant associations, and the physical position of some associations suggested two possible candidate genes. An Orange (Or) gene was a possible candidate for visual color evaluation and the α- and β-carotene contents. Sanger sequencing detected a new allele of Or with an SNP which caused a non-synonymous amino acid substitution. Genotypes of this SNP corresponded to the visual evaluation of root color in another breeding line. A chromoplast-specific lycopene β-cyclase (CYC-B) gene was a possible candidate for the β/α carotene ratio. On CYC-B, five amino acid substitutions were detected between parental plants of the F2 population. The detected associations and SNPs on the possible candidate genes will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots.

scholarly journals GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton (Gossypium hirsutum L.) Across Multiple Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Zareen Sarfraz ◽  
Muhammad Shahid Iqbal ◽  
Xiaoli Geng ◽  
Muhammad Sajid Iqbal ◽  
Mian Faisal Nazir ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Fiber Quality ◽  
Hybrid Vigor ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome ◽  
Improvement Programs ◽  
Multiple Environments

For about a century, plant breeding has widely exploited the heterosis phenomenon–often considered as hybrid vigor–to increase agricultural productivity. The ensuing F1 hybrids can substantially outperform their progenitors due to heterozygous combinations that mitigate deleterious mutations occurring in each genome. However, only fragmented knowledge is available concerning the underlying genes and processes that foster heterosis. Although cotton is among the highly valued crops, its improvement programs that involve the exploitation of heterosis are still limited in terms of significant accomplishments to make it broadly applicable in different agro-ecological zones. Here, F1 hybrids were derived from mating a diverse Upland Cotton germplasm with commercially valuable cultivars in the Line × Tester fashion and evaluated across multiple environments for 10 measurable traits. These traits were dissected into five different heterosis types and specific combining ability (SCA). Subsequent genome-wide predictions along-with association analyses uncovered a set of 298 highly significant key single nucleotide polymorphisms (SNPs)/Quantitative Trait Nucleotides (QTNs) and 271 heterotic Quantitative Trait Nucleotides (hQTNs) related to agronomic and fiber quality traits. The integration of a genome wide association study with RNA-sequence analysis yielded 275 candidate genes in the vicinity of key SNPs/QTNs. Fiber micronaire (MIC) and lint percentage (LP) had the maximum number of associated genes, i.e., each with 45 related to QTNs/hQTNs. A total of 54 putative candidate genes were identified in association with HETEROSIS of quoted traits. The novel players in the heterosis mechanism highlighted in this study may prove to be scientifically and biologically important for cotton biologists, and for those breeders engaged in cotton fiber and yield improvement programs.

scholarly journals Genome-Wide Association Analysis of Plant Height Using the Maize F1 Population

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 432 ◽  
Author(s):  
Zhang ◽  
Wan ◽  
He ◽  
Lan ◽  
Li
Keyword(s):  
Candidate Genes ◽  
Plant Height ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Plant Density ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Higher Plant ◽  
Genome Wide ◽  
A Genome

Drastic changes in plant height (PH) are observed when maize adapt to a higher plant density. Most importantly, PH is an important factor affecting maize yield. Although the genetic basis of PH has been extensively studied using different populations during the past decades, genetic basis remains unclear in the F1 population, which was a widely used population in production. In this study, a genome-wide association study (GWAS) was conducted using an F1 population consisting of 300 maize hybrids with 17,652 single nucleotide polymorphisms (SNPs) makers to identify candidate genes for controlling PH. A total of nine significant SNPs makers and two candidate genes were identified for PH. The candidate genes, Zm00001d018617 and Zm00001d023659, were the genes most probable to be involved in the development of PH. Our results provide new insights into the genetic basis of PH in maize.

scholarly journals Exploring the genetic architecture of feed efficiency traits in chickens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jorge Augusto Petroli Marchesi ◽  
Rafael Keith Ono ◽  
Maurício Egídio Cantão ◽  
Adriana Mércia Guaratini Ibelli ◽  
Jane de Oliveira Peixoto ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Feed Efficiency ◽  
Gene Networks ◽  
Genome Wide Association Study ◽  
Body Weight Gain ◽  
Snp Array ◽  
Experimental Population ◽  
Economic Traits ◽  
A Genome ◽  
Genomic Regions

AbstractChicken feed efficiency (FE) traits are the most important economic traits in broiler production. Several studies evaluating genetic factors affecting food consumption in chickens are available. However, most of these studies identified genomic regions containing putative quantitative trait loci for each trait separately. It is still a challenge to find common gene networks related to these traits. Therefore, here, a genome-wide association study (GWAS) was conducted to explore candidate genomic regions responsible for Feed Intake (FI), Body Weight Gain (BWG) and Feed Conversion Ratio (FCR) traits and their gene networks. A total of 1430 broilers from an experimental population was genotyped with the high density Affymetrix 600K SNP array. A total of 119 associated SNPs located in 20 chromosomes were identified, where some of them were common in more than one FE trait. In addition, novel genomic regions were prospected considering the SNPs dominance effects and sex interaction, identifying putative candidate genes only when these effects were fit in the model. Relevant candidate genes such as ATRNL1, PIK3C2A, PTPRN2, SORCS3 and gga-mir-1759 were highlighted in this study helping to elucidate the genomic architecture of feed efficiency traits. These results provide new insights on the mechanisms underlying the consumption and utilization of food in chickens.

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