A GWAS approach to find SNPs associated with salt removal in rice leaf sheath

Abstract Background and Aims The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice. Methods In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl– concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress. Key results For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress. Conclusions These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.

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

Animals ◽

10.3390/ani11010192 ◽

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.

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

Genes ◽

10.3390/genes12121897 ◽

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.

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

10.22541/au.161165160.08519096/v1 ◽

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.

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

Genes ◽

10.3390/genes10100803 ◽

2019 ◽

Vol 10 (10) ◽

pp. 803 ◽

Cited By ~ 1

Author(s):

Wang ◽

Yan ◽

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.

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Single-Nucleotide Polymorphism Variations Associated With Specific Genes Putatively Identified Enhanced Genetic Predisposition for 305-Day Milk Yield in the Girolando Crossbreed

Frontiers in Genetics ◽

10.3389/fgene.2020.573344 ◽

2021 ◽

Vol 11 ◽

Author(s):

Alex Silva da Cruz ◽

Danilo Conrado Silva ◽

Lysa Bernardes Minasi ◽

Larissa Kamídia de Farias Teixeira ◽

Flávia Melo Rodrigues ◽

...

Keyword(s):

Milk Production ◽

Milk Yield ◽

Genetic Predisposition ◽

Fixed Effects ◽

Genome Wide Association Study ◽

Significant Snps ◽

Nucleotide Polymorphisms ◽

Production Traits ◽

Single Nucleotide ◽

A Genome

Milk production phenotypes are the main focus of genetic selection in dairy herds, and although there are many genes identified as related to the biology of these traits in pure breeds, little is known about crossbreed animals. This study aimed to identify potential genes associated with the 305-day milk yield in 337 crossbreed Gir × Holstein (Girolando) animals. Milk production records were genotyped for 45,613 single-nucleotide polymorphisms (SNPs). This dataset was used for a genome-wide association study (GWAS) using the 305-day milk yield adjusted for the fixed effects of herd and year and linear and quadratic effects of age at calving (in days) and calving factor averaged per animal. Genes within the significant SNPs were retrieved from the Bos taurus ARS-UCD1.2 assembly (bosTau9) for gene ontology analysis. In summary, the GWAS identified 52 SNPs associated [p ≤ 10–4, false discovery rate (FDR) = 8.77%] with milk production, including NUB1 and SLC24A2, which were previously described as related to milk production traits in cattle. The results suggest that SNPs associated mainly with NUB1 and SLC24A2 could be useful to understand milk production in Girolando and used as predictive markers for selecting genetic predisposition for milk yield in Girolando.

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.770434 ◽

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.

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

10.21203/rs.3.rs-1014140/v1 ◽

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.

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.565552 ◽

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.

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Identification of SNPs and Candidate Genes for Milk Produce Ability in Yorkshire Pig

10.21203/rs.3.rs-585023/v1 ◽

2021 ◽

Author(s):

Lijun Shi ◽

Yang Li ◽

Qian Liu ◽

Longchao Zhang ◽

Ligang Wang ◽

...

Keyword(s):

Candidate Genes ◽

Milk Fat ◽

Genome Wide Association Study ◽

Random Effect ◽

Random Effect Model ◽

Significant Snps ◽

Limiting Factor ◽

Lactation Performance ◽

Genome Wide ◽

A Genome

Abstract Background: Sow milk produce ability is an important limiting factor impacting suboptimal growth and survival of piglets. By pig genetic improvement, the litter size has been increased, and larger litters need more suckled mammary glands, that results in increased milk from lactating sow. Hence, it has much significance to explore the sow lactation performance. The aim of this study was to estimate genetic parameters and screen single nucleotide polymorphisms (SNPs) for milk produce ability trait in 985 Yorkshire pigs by a genome-wide association study (GWAS), and to further identify the candidate genes.Results: By ASReml, we estimated the heritability of sow milk produce ability: 0.18 ± 0.07. With the Fixed and random effect model Circulating Probability Unification (FarmCPU), we performed a GWAS, and detected seven genome-wide significant SNPs, namely, Sus scrofa Chromosome (SSC) 2: ASGA0010040 (P = 7.73E-11); SSC2:MARC0029355 (P = 1.30E-08), SSC6: WU_10.2_6_65751151 (P = 1.32E-10), SSC7: MARC0058875 (P = 4.99E-09), SSC10: WU_10.2_10_49571394 (P = 6.79E-08), SSC11: M1GA0014659 (P = 1.19E-07), and SSC15: MARC0042106 (P = 1.16E-07). We performed the distribution of phenotypes corresponding to genotypes of the seven SNPs, and showed that ASGA0010040, MARC0029355, MARC0058875, WU_10.2_10_49571394, M1GA0014659, and MARC0042106 have extreme phenotypic values corresponded to the homozygous genotypes, while the intermediate values corresponded to the heterozygous genotypes. Further, we screened for flanking regions ± 200 kb nearby seven significant SNPs, and identified 30 genes. Among of them, 24 as the candidates were involved in lactose metabolism, colostrum immunity, milk protein, and milk fat by the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis. Through the combined analysis between 24 candidate genes and differently expressed genes (DEGs) detected in transcriptome data (GSE101983), we found 11 commons (NAV2, ANO3, MUC15, DISP3, FBXO6, CLCN6, SLA-DQB1, PSMB8, PSMB9, TAP1, and KIF5C). Further, by comparing the chromosome positions of the candidate genes with the quantitative trait locus (QTLs) previously reported, a total of 13 genes were found to be within 0.86 Mb to 93.92 Mb of the reported QTLs for sow milk yield, in which, NAV2 was found to be located with 0.86 Mb of the QTL region ssc2: 40936355.Conclusions: In conclusion, we identified seven significant SNPs located on SSC2, 6, 7, 10, 11, and 15, and proposed 24 candidate genes for milk produce ability trait in Yorkshire pig. Among of them, 11 were the key candidates. These results contribute to the identification of variants and candidate genes for sow milk produce ability.

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Genome-wide association mapping for agronomic and quality traits in foxtail millet

10.21203/rs.2.10042/v1 ◽

2019 ◽

Author(s):

Yanhong Lou ◽

Yun Chen ◽

Zhihao Liu ◽

Mingjie Sun ◽

Fei Han ◽

...

Keyword(s):

Genome Wide Association Study ◽

Foxtail Millet ◽

Significant Snps ◽

Genomic Variation ◽

Genome Wide Association ◽

Quality Traits ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Genome Wide ◽

A Genome

Abstract Background: Foxtail millet [Setaria italica (L.) P. Beauv.] is a particularly important cereal and fodder crop in arid and semi-arid regions. The genomic variation and alleles underpinning agronomic and quality traits are important for foxtail millet improvement. To better understand the diversity of foxtail millet and facilitate the genetic dissection of its agronomic and quality traits, we used high-quality single nucleotide polymorphisms (SNPs) to perform a genome-wide association study (GWAS). Results: Using genotyping-by-sequencing, 107 foxtail millet accessions were sequenced, and further analysis revealed 72,181 high-quality SNPs, of which 53 were significantly associated with 15 agronomic and quality traits. These SNPs were distributed across the nine chromosomes of foxtail millet; 44 were located in intergenic regions, whereas one and eight SNPs were located in exon and intron regions, respectively. The GWAS revealed that 28 SNPs were associated with a single trait. Conclusions: For some of the significant SNPs, favourable genotypes showed pyramiding effects for several traits. The 53 loci identified in this study will therefore be useful for breeding programs aimed at foxtail millet improvement.

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