Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis

Abstract Background Understanding the complexity of the vine plant’s response to water deficit represents a major challenge for sustainable winegrowing. Regulation of water use requires a coordinated action between scions and rootstocks on which cultivars are generally grafted to cope with phylloxera infestations. In this regard, a genome-wide association study (GWAS) approach was applied on an ‘ad hoc’ association mapping panel including different Vitis species, in order to dissect the genetic basis of transpiration-related traits and to identify genomic regions of grape rootstocks associated with drought tolerance mechanisms. The panel was genotyped with the GrapeReSeq Illumina 20 K SNP array and SSR markers, and infrared thermography was applied to estimate stomatal conductance values during progressive water deficit. Results In the association panel the level of genetic diversity was substantially lower for SNPs loci (0.32) than for SSR (0.87). GWAS detected 24 significant marker-trait associations along the various stages of drought-stress experiment and 13 candidate genes with a feasible role in drought response were identified. Gene expression analysis proved that three of these genes (VIT_13s0019g03040, VIT_17s0000g08960, VIT_18s0001g15390) were actually induced by drought stress. Genetic variation of VIT_17s0000g08960 coding for a raffinose synthase was further investigated by resequencing the gene of 85 individuals since a SNP located in the region (chr17_10,497,222_C_T) was significantly associated with stomatal conductance. Conclusions Our results represent a step forward towards the dissection of genetic basis that modulate the response to water deprivation in grape rootstocks. The knowledge derived from this study may be useful to exploit genotypic and phenotypic diversity in practical applications and to assist further investigations.

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Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens

Scientific Reports ◽

10.1038/s41598-021-86176-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Juniper A. Lake ◽

Jack C. M. Dekkers ◽

Behnam Abasht

Keyword(s):

Candidate Genes ◽

Broiler Chickens ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Specific Protein ◽

Chromosome 11 ◽

A Genome ◽

White Striping ◽

Commercial Broiler ◽

Wooden Breast

AbstractWooden breast (WB) and white striping (WS) are highly prevalent and economically damaging muscle disorders of modern commercial broiler chickens characterized respectively by palpable firmness and fatty white striations running parallel to the muscle fiber. High feed efficiency and rapid growth, especially of the breast muscle, are believed to contribute to development of such muscle defects; however, their etiology remains poorly understood. To gain insight into the genetic basis of these myopathies, a genome-wide association study was conducted using a commercial crossbred broiler population (n = 1193). Heritability was estimated at 0.5 for WB and WS with high genetic correlation between them (0.88). GWAS revealed 28 quantitative trait loci (QTL) on five chromosomes for WB and 6 QTL on one chromosome for WS, with the majority of QTL for both myopathies located in a ~ 8 Mb region of chromosome 5. This region has highly conserved synteny with a portion of human chromosome 11 containing a cluster of imprinted genes associated with growth and metabolic disorders such as type 2 diabetes and Beckwith-Wiedemann syndrome. Candidate genes include potassium voltage-gated channel subfamily Q member 1 (KCNQ1), involved in insulin secretion and cardiac electrical activity, lymphocyte-specific protein 1 (LSP1), involved in inflammation and immune response.

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Variability among Young Table Grape Cultivars in Response to Water Deficit and Water Use Efficiency

Agronomy ◽

10.3390/agronomy9030135 ◽

2019 ◽

Vol 9 (3) ◽

pp. 135 ◽

Cited By ~ 3

Author(s):

Carolin Weiler ◽

Nikolaus Merkt ◽

Jens Hartung ◽

Simone Graeff-Hönninger

Keyword(s):

Stomatal Conductance ◽

Gas Exchange ◽

Water Deficit ◽

Water Use ◽

Dry Mass ◽

Table Grape ◽

Water Limitation ◽

Use Efficiency ◽

Response To Water ◽

Grape Cultivars

Climate change will lead to higher frequencies and durations of water limitations during the growing season, which may affect table grape yield. The aim of this experiment was to determine the variability among 3-year old table grape cultivars under the influence of prolonged water deficit during fruit development on gas exchange, growth, and water use efficiency. Six own rooted, potted table grape cultivars (cv. ‘Muscat Bleu’, ‘Fanny’, ‘Nero’, ‘Palatina’, ‘Crimson Seedless’ and ‘Thompson Seedless’) were subjected to three water deficit treatments (Control treatment with daily irrigation to 75% of available water capacity (AWC), moderate (50% AWC), and severe water deficit treatment (25% AWC)) for three consecutive years during vegetative growth/fruit development. Water deficit reduced assimilation, stomatal conductance, and transpiration, and increased water use efficiencies (WUE) with severity of water limitation. While leaf area and number of leaves were not affected by treatments in any of the tested cultivars, the response of specific leaf area to water deficit depended on the cultivar. Plant dry mass decreased with increasing water limitation. Overall, high variability of cultivars to gas exchange and water use efficiencies in response to water limitation was observed. ’Palatina’ was the cultivar having a high productivity (high net assimilation) and low water use (low stomatal conductance) and the cultivar ‘Fanny’ was characterized by the highest amount of total annual dry mass as well as the highest total dry mass production per water supplied during the experiment (WUEDM). Hence, ‘Fanny’ and ‘Palatina’ have shown to be cultivars able to cope with water limiting conditions and should be extensively tested in further studies.

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Physiological responses of two halophytic grass species under drought stress environment

Acta Botanica Croatica ◽

10.1515/botcro-2016-0018 ◽

2016 ◽

Vol 75 (1) ◽

pp. 31-38 ◽

Cited By ~ 9

Author(s):

Zamin Shaheed Siddiqui ◽

Huda Shahid ◽

Jung-Il Cho ◽

Sung-Han Park ◽

Tae-Hun Ryu ◽

...

Keyword(s):

Drought Stress ◽

Stomatal Conductance ◽

Water Deficit ◽

Physiological Responses ◽

Biomass Accumulation ◽

Photosynthetic Performance ◽

Grass Species ◽

Free Proline ◽

Relative Water ◽

Halophytic Grasses

AbstractThe physiological responses of two halophytic grass species, Halopyrum mucronatum (L.) Staph. and Cenchrus ciliaris (L.), under drought stress were evaluated. Biomass accumulation, relative water content, free proline, H2O2content, stomatal conductance, photosynthetic performance and quantum yield (Fv/Fmratio) were studied. Under drought conditions, these halophytic plants expressed differential responses to water deficit. Stomatal conductance and free proline content were higher in H. mucronatum than in C. ciliaris, while H2O2content in H. mucronatum was substantially lower than in C. ciliaris. Performance index showed considerable sensitivity to a water deficit condition, more so in C. ciliaris than in H. mucronatum. Results were discussed in relation to comparative physiological performance and antioxidant enzymes activity of both halophytic grasses under drought stress.

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Genome-Wide Association Studies of Leaf Angle in Maize

10.21203/rs.3.rs-329481/v1 ◽

2021 ◽

Author(s):

Bo Peng ◽

Xiaolei Zhao ◽

Yi Wang ◽

Chunhui Li ◽

Yongxiang Li ◽

...

Keyword(s):

Candidate Genes ◽

Phenotypic Variation ◽

Genetic Basis ◽

Genome Wide Association ◽

Leaf Angle ◽

Genome Wide Association Studies ◽

Major Qtls ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome

Abstract Compact plant-type with small leaf angle has increased canopy light interception, which is conducive to the photosynthesis of the population and higher population yield at high density planting in maize. In this study, a panel of 285 diverse maize inbred lines genotyped with 56,000 SNPs was used to investigate the genetic basis of leaf angle across three consecutive years using a genome-wide association study (GWAS). The leaf angle showed broad phenotypic variation and high heritability across different years. Population structure analysis subdivided the panel into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Tangsipingtou, Reid, Lancaster and P. When tested with the optimal GWAS model, we found that the Q+K model was the best in reducing false positive. In total, 96 SNPs accounting for 5.54%-10.44% of phenotypic variation were significantly (P<0.0001) associated with leaf angle across three years. According to the linkage disequilibrium decay distance, 96 SNPs were binned in 43 QTLs for leaf angle. Seven major QTLs with R2>8% stably detected in at least two years and BLUP values were clustered in four genomic regions (bins 2.01, 2.07, 5.06, and 10.04). Seven important candidate genes, Zm00001d001961, Zm00001d006348, Zm00001d006463, Zm00001d017618, Zm00001d024919, Zm00001d025018, and Zm00001d025033 were predicted for the seven stable major QTLs, respectively. The markers identified in this study can be used for molecular breeding for leaf angle, and the candidate genes would contribute to further understanding of the genetic basis of leaf angle.

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Genome-Wide Association Study Reveals Candidate Genes Involved in Fruit Trait Variation in Persian Walnut (Juglans regia L.)

Frontiers in Plant Science ◽

10.3389/fpls.2020.607213 ◽

2021 ◽

Vol 11 ◽

Author(s):

Anthony Bernard ◽

Julie Crabier ◽

Armel S. L. Donkpegan ◽

Annarita Marrano ◽

Fabrice Lheureux ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Fruit Quality ◽

Genome Wide Association Study ◽

Juglans Regia ◽

Snp Array ◽

Germplasm Collection ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

Elucidating the genetic determinants of fruit quality traits in walnut is essential to breed new cultivars meeting the producers and consumers’ needs. We conducted a genome-wide association study (GWAS) using multi-locus models in a panel of 170 accessions of Juglans regia from the INRAE walnut germplasm collection, previously genotyped using the AxiomTMJ. regia 700K SNP array. We phenotyped the panel for 25 fruit traits related to morphometrics, shape, volume, weight, ease of cracking, and nutritional composition. We found more than 60 marker-trait associations (MTAs), including a highly significant SNP associated with nut face diameter, nut volume and kernel volume on chromosome 14, and 5 additional associations were detected for walnut weight. We proposed several candidate genes involved in nut characteristics, such as a gene coding for a beta-galactosidase linked to several size-related traits and known to be involved in fruit development in other species. We also confirmed associations on chromosomes 5 and 11 with nut suture strength, recently reported by the University of California, Davis. Our results enhance knowledge of the genetic control of important agronomic traits related to fruit quality in walnut, and pave the way for the development of molecular markers for future assisted selection.

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GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

10.21203/rs.2.10682/v5 ◽

2020 ◽

Author(s):

Min Yao ◽

Mei Guan ◽

Zhenqian Zhang ◽

Qiuping Zhang ◽

Yixin Cui ◽

...

Keyword(s):

Oleic Acid ◽

Candidate Genes ◽

Acid Content ◽

Complex Traits ◽

Snp Array ◽

Oleic Acid Content ◽

Crop Species ◽

Genome Wide ◽

A Genome ◽

Chromosome Haplotype

Abstract Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We use the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes ( BnmtACP2-A02 , BnABCI13-A02 and BnECI1-A02 ) in the A02 chromosome haplotype region and two genes ( BnFAD8-C02 and BnSDP1-C02 ) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

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Genome-wide association mapping for high temperature tolerance in wheat through 90k SNP array using physiological and yield traits

PLoS ONE ◽

10.1371/journal.pone.0262569 ◽

2022 ◽

Vol 17 (1) ◽

pp. e0262569

Author(s):

Hafiz Ghulam Muhu-Din Ahmed ◽

Muhammad Naeem ◽

Yawen Zeng ◽

Muhammad Abdul Rehman Rashid ◽

Aziz Ullah ◽

...

Keyword(s):

Heat Stress ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Wheat Yield ◽

Snp Array ◽

Genome Wide Association ◽

Strong Positive Correlation ◽

Yield Traits ◽

Genome Wide ◽

A Genome

Dissecting the genetic basis of physiological and yield traits against tolerance to heat stress is an essential in wheat breeding programs to boost up the wheat yield for sustainable food security. Herein, a genome-wide association study (GWAS) was performed to reveal the genetic basis of heat tolerance using high-density Illumina 90K Infinium SNPs array through physiological and yield indices. These indices were phenotyped on a diverse panel of foreign and domestic genotypes of Pakistan, grown in normal and heat-stressed environments. Based on STRUCTURE analysis, the studied germplasm clustered into four sub-population. Highly significant variations with a range of moderate (58.3%) to high (77.8%) heritability was observed under both conditions. Strong positive correlation existed among physiological and yield related attributes. A total of 320 significant (-log10 P ≥ 3) marker-trait associations (MTAs) were identified for the observed characters. Out of them 169 and 151 MTAs were recorded in normal and heat stress environments, respectively. Among the MTA loci, three (RAC875_c103017_302, Tdurum_contig42087_1199, and Tdurum_contig46877_488 on chromosomes 4B, 6B, and 7B respectively), two (BobWhite_c836_422 and BS00010616_51) and three (Kukri_rep_c87210_361, D_GA8KES401BNLTU_253 and Tdurum_contig1015_131) on chromosomes 5A, 1B, and 3D at the positions 243.59cM, 77.82cM and 292.51cM) showed pleiotropic effects in studied traits under normal, heat-stressed and both conditions respectively. The present study not only authenticated the numerous previously reported MTAs for examined attributes but also revealed novel MTAs under heat-stressed conditions. Identified SNPs will be beneficial in determining the novel genes in wheat to develop the heat tolerant and best yielded genotypes to fulfill the wheat requirement for the growing population.

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GWAS Analysis of Wheat Pre-breeding Germplasm for Terminal Drought Stress Using Next Generation Sequencing Technology

10.20944/preprints202002.0272.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sajid Shokat ◽

Deepmala Sehgal ◽

Fulai Liu ◽

Sukhwinder Singh

Keyword(s):

Drought Stress ◽

Candidate Genes ◽

Vegetation Index ◽

Genome Wide Association Study ◽

Potential Candidate ◽

Terminal Drought ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome ◽

Terminal Drought Stress

Bread wheat (Triticum aestivum L.) is one of the most important cereal crops for food security. Of all the stresses that curtail wheat productivity, drought has the most detrimental effects. Especially terminal drought stress i.e. at the time of flowering imposes a big challenge to sustain grain production. In the current study, 339 pre-breeding lines derived from three-way crosses of exotics x elite lines were evaluated in the irrigated and drought stress environments at Obregon, Mexico for the year 2016 and 2018. Drought significantly reduced yield (Y), spike length (SL), number of grains per spikes (NGS) and thousand kernel weight (TKW) by 46.4, 19.2, 23.5 and 25.9%, respectively in comparison to irrigated conditions. Kernel abortion (KA), highly correlated with Y, increased significantly (11.6%) under drought stress environment. Population structure analysis in this panel revealed three sub-populations and a genome wide linkage disequilibrium (LD) decay was at 2.5 cM. Single marker and haplotypes-based genome wide association study (GWAS) revealed significant associations on three chromosomes; 4A (HB10.7), 2D (HB6.10) and 3B (HB8.12) with Y, SL and TKW, respectively. Likewise, associations on chromosomes 6B (HB17.1) and 3A (HB7.11) were identified for NGS and on 3A (HB7.12) for KA. Five traits i.e. normalized difference vegetation index (NDVI), canopy temperature depression (CTD) days to heading (DTH), NGS, KA were associated at chromosome 3A both under irrigated and drought conditions however, different haplotypes were estimated. Twenty-six SNPs were part of 10 haplotype blocks associated with Y, SL, TKW, NGS and KA. In silico analysis of the associated SNPs/haplotypes showed hits with candidate genes known to confer abiotic stress resistance in model species and crops. Potential candidate genes include those coding for sulfite exporter TauE/SafE family in Arabidopsis thaliana, TBC domain containing protein in Oryza sativa subsp. Japonica and heat shock proteins in Aegilops tauschii subsp. tauschii were revealed. The SNPs linked to the promising genes identified in the study can be used for marker-assisted selection.

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Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes

10.1101/2021.05.06.442962 ◽

2021 ◽

Author(s):

Charles Pignon ◽

Samuel Fernandes ◽

Ravi Valluru ◽

Nonoy Bandillo ◽

Roberto Lozano ◽

...

Keyword(s):

Stomatal Conductance ◽

Light Intensity ◽

Water Use Efficiency ◽

Candidate Genes ◽

Water Use ◽

Thermal Imaging ◽

Genetic Basis ◽

Photosynthetic Gas Exchange ◽

Chlorophyll Metabolism ◽

Use Efficiency

Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential to maintenance of water-use efficiency (WUE). However, little is known about the genetic basis for natural variation in stomatal movement, especially in C4 crops. This is partly because the stomatal response to a change in light intensity is difficult to measure at the scale required for association studies. High-throughput thermal imaging was used to bypass the phenotyping bottleneck and assess 10 traits describing stomatal conductance (gs) before, during and after a stepwise decrease in light intensity for a diversity panel of 659 sorghum accessions. Results from thermal imaging significantly correlated with photosynthetic gas-exchange measurements. gs traits varied substantially across the population and were moderately heritable (h2 up to 0.72). An integrated genome-wide and transcriptome-wide association study (GWAS/TWAS) identified candidate genes putatively driving variation in stomatal conductance traits. Of the 239 unique candidate genes identified with greatest confidence, 77 were orthologs of Arabidopsis genes related to functions implicated in WUE, including stomatal opening/closing (24 genes), stomatal/epidermal cell development (35 genes), leaf/vasculature development (12 genes), or chlorophyll metabolism/photosynthesis (8 genes). These findings demonstrate an approach to finding genotype-to-phenotype relationships for a challenging trait as well as candidate genes for further investigation of the genetic basis of WUE in a model C4 grass for bioenergy, food, and forage production.

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