scholarly journals Identification and Confirmation of Loci Associated With Canopy Wilting in Soybean Using Genome-Wide Association Mapping

2021 ◽  
Vol 12 ◽  
Author(s):  
Siva K. Chamarthi ◽  
Avjinder S. Kaler ◽  
Hussein Abdel-Haleem ◽  
Felix B. Fritschi ◽  
Jason D. Gillman ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Association Mapping ◽  
Candidate Genes ◽  
Stress Responses ◽  
Water Conservation ◽  
Production Systems ◽  
Block Design ◽  
Plant Stress ◽  
Significant Snps ◽  
Nucleotide Polymorphisms

Drought causes significant soybean [Glycine max (L.) Merr.] yield losses each year in rain-fed production systems of many regions. Genetic improvement of soybean for drought tolerance is a cost-effective approach to stabilize yield under rain-fed management. The objectives of this study were to confirm previously reported soybean loci and to identify novel loci associated with canopy wilting (CW) using a panel of 200 diverse maturity group (MG) IV accessions. These 200 accessions along with six checks were planted at six site-years using an augmented incomplete block design with three replications under irrigated and rain-fed treatments. Association mapping, using 34,680 single nucleotide polymorphisms (SNPs), identified 188 significant SNPs associated with CW that likely tagged 152 loci. This includes 87 SNPs coincident with previous studies that likely tagged 68 loci and 101 novel SNPs that likely tagged 84 loci. We also determined the ability of genomic estimated breeding values (GEBVs) from previous research studies to predict CW in different genotypes and environments. A positive relationship (P ≤ 0.05;0.37 ≤ r ≤ 0.5) was found between observed CW and GEBVs. In the vicinity of 188 significant SNPs, 183 candidate genes were identified for both coincident SNPs and novel SNPs. Among these 183 candidate genes, 57 SNPs were present within genes coding for proteins with biological functions involved in plant stress responses. These genes may be directly or indirectly associated with transpiration or water conservation. The confirmed genomic regions may be an important resource for pyramiding favorable alleles and, as candidates for genomic selection, enhancing soybean drought tolerance.

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.

Polymorphisms in intron 1 of carrot AOX2b – a useful tool to develop a functional marker?

2011 ◽  
Vol 9 (2) ◽  
pp. 177-180 ◽  
Author(s):  
Hélia Cardoso ◽  
Maria Doroteia Campos ◽  
Thomas Nothnagel ◽  
Birgit Arnholdt-Schmitt
Keyword(s):  
Stress Responses ◽  
Agronomic Traits ◽  
Gene Diversity ◽  
Plant Stress ◽  
Functional Marker ◽  
Functional Markers ◽  
Length Variation ◽  
Nucleotide Polymorphisms ◽  
Intron 1 ◽  
Stress Behaviour

Alternative oxidase (AOX) has been proposed as a promising functional marker candidate for multiple plant stress behaviour. The present paper describes natural polymorphism in AOX2b of Daucus carota L. (DcAOX2b). Exon-primed intron crossing-PCR (EPIC-PCR) revealed length variation (intron length polymorphisms, ILPs) in intron 1. Six fragment patterns were identified in 40 genotypes. However, no more than two fragments were found per genotype, suggesting the presence of two alleles. The ILPs were able to discriminate between single plant genotypes in cv. Rotin and to distinguish individual wild carrot plants. The repetitive pattern of intron 1 length variation allows the grouping of genotypes for functional analysis in future studies. Sequence analysis in intron 1 of polymorphic but also of obviously identical PCR-fragments revealed underlying high levels of sequence polymorphisms between alleles and genotypes. Variation was due to repetitive insertion/deletion (InDel) events and single-nucleotide polymorphisms (SNPs). The results suggest that high AOX2b gene diversity in D. carota may be a source of functional markers for agronomic traits related to environmental stress responses.

Phytocystatins and their Potential Application in the Development of Drought Tolerance Plants in Soybeans (Glycine max L.)

2020 ◽  
Vol 27 (2) ◽  
pp. 135-144 ◽  
Author(s):  
Phetole Mangena
Keyword(s):  
Abiotic Stress ◽  
Drought Tolerance ◽  
Stress Responses ◽  
Plant Stress ◽  
Cysteine Proteases ◽  
Industrial Applications ◽  
Stress Factors ◽  
Soybean Plant ◽  
Oilseed Crop ◽  
The Impact

: Plant cystatins, also called phytocystatins constitute a family of specific cysteine protease inhibitors found in several monocots and dicots. In soybean, phytocystatins regulate several endogenous processes contributing immensely to this crop’s tolerance to abiotic stress factors. Soybeans offer numerous nutritional, pharmaceutical and industrial benefits; however, their growth and yields is hampered by drought, which causes more than 10% yield losses recorded every harvest period worldwide. This review analyses the role of papain-like cysteine proteases and their inhibitors in soybean plant growth and development under drought stress. It also describes their localisation, regulation, target organs and tissues, and the overall impact of cystatins on generating drought tolerance soybean plants. These proteins have many functions that remain poorly characterized, particularly under abiotic stress. Although much information is available on the utilisation of proteases for industrial applications, very few reports have focused on the impact of proteases on plant stress responses. The exploitation of cystatins in plant engineering, as competitive proteases inhibitors is one of the means that will guarantee the continued utilisation of soybeans as an important oilseed crop.

scholarly journals Genome-wide association mapping of sodium and potassium concentration in rice grains and shoots under alternate wetting and drying and continuously flooded irrigation

2021 ◽  
Author(s):  
Caijin Chen ◽  
Anthony J. Travis ◽  
Mahmud Hossain ◽  
Md Rafiqul Islam ◽  
Adam H. Price ◽  
...  
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Mixed Model ◽  
Significant Snps ◽  
Field Conditions ◽  
Genome Wide Association ◽  
Wetting And Drying ◽  
Alternate Wetting And Drying ◽  
Genome Wide ◽  
Monovalent Ions

Abstract Key message Identification of a large number of QTL and candidate genes for sodium accumulation in a field grown population of rice derived from theaus subpopulation. Abstract Rice (Oryza sativa L.) is a globally important cereal crop. Sodium (Na+) and potassium (K+) are the major monovalent ions which affect rice growth, and exploring their uptake mechanisms will be useful for understanding rice biology. Since the balance of Na+ and K+ plays a significant role in adaptation of rice to salinity, that biology might inform the search for tolerance. In this study, the Na+ and K+ concentration and Na+/K+ ratio in grains and shoots were analyzed in the Bengal and Assam Aus Panel grown in field conditions under continuously flooded (CF) and alternate wetting and drying (AWD) irrigation. Overall, AWD irrigation significantly reduced the Na+ concentration and increased the K+ concentration in shoots and grains compared to the plants grown under CF. Genome-wide association mapping was conducted on Na+, K+ concentration and Na+/K+ ratio with 2 million SNPs using an efficient mixed model. Only QTLs which contained more than two significant SNPs (p < 0.0001) and where at least one of these significant SNPs passed a 10% false discovery rate were reported. A total of 106 QTLs were identified as being associated with Na+ concentration and Na+/K+ ratio across all traits and field conditions, with 48 QTLs found in multiple traits and/or water conditions. Four notable QTLs (one each on chromosomes 1 and 11, two on chromosome 2) and the haplotype variants of four candidate genes (OsHKT1;5, OsNHX2, LOC_Os02g32490 and OsFAD2_1) are discussed. The QTLs/candidate genes identified here could be useful for breeding rice that accumulates lower concentrations of sodium.

scholarly journals Association Mapping and Nucleotide Sequence Variation in Five Drought Tolerance Candidate Genes in Spring Wheat

2013 ◽  
Vol 6 (2) ◽  
Author(s):  
Erena A. Edae ◽  
Patrick F. Byrne ◽  
Harish Manmathan ◽  
Scott D. Haley ◽  
Marc Moragues ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Drought Tolerance ◽  
Association Mapping ◽  
Candidate Genes ◽  
Spring Wheat ◽  
Sequence Variation ◽  
Nucleotide Sequence Variation

scholarly journals Identification of Markers Associated with Yield Traits and Morphological Features in Maize (Zea mays L.)

Plants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 330 ◽  
Author(s):  
Agnieszka Tomkowiak ◽  
Jan Bocianowski ◽  
Łukasz Wolko ◽  
Józef Adamczyk ◽  
Sylwia Mikołajczyk ◽  
...  
Keyword(s):  
Association Mapping ◽  
Principal Component ◽  
Significant Snps ◽  
Mixed Linear Model ◽  
Inbred Lines ◽  
Flowering Plants ◽  
Morphological Features ◽  
Yield Traits ◽  
Nucleotide Polymorphisms ◽  
Lateral Branches

Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium in molecular plant breeding. The aim of this study was the identification of single nucleotide polymorphisms (SNPs) and SilicoDArT markers associated with yield traits and morphological features in maize. Plant material constituted inbred lines. The field experiment with inbred lines was established on 10 m2 plots in a set of complete random blocks in three replicates. We observed 22 quantitative traits. Association mapping was performed in this study using a method based on the mixed linear model with the population structure estimated by eigenanalysis (principal component analysis applied to all markers) and modeled by random effects. As a result of mapping, 969 markers (346 SNPs and 623 SilocoDArT) were selected from 49,911 identified polymorphic molecular markers, which were significantly associated with the analyzed morphological features and yield structure traits. Markers associated with five or six traits were selected during further analyses, including SilicoDArT 4591115 (anthocyanin coloration of anthers, length of main axis above the highest lateral branch, cob length, number of grains per cob, weight of fresh grains per cob and weight of fresh grains per cob at 15% moisture), SilicoDArT 7059939 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, time of silk emergence—50% of flowering plants, anthocyanin coloration of anthers and cob diameter), SilicoDArT 5587991 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, anthocyanin coloration of anthers, curvature of lateral branches and number of rows of grain). The two genetic similarity dendrograms between the inbred lines were constructed based on all significant SNPs and SilicoDArT markers. On both dendrograms lines clustered according to the kernel structure (flint, dent) and origin. The selected markers may be useful in predicting hybrid formulas in a heterosis culture. The present study demonstrated that molecular SNP and Silico DArT markers could be used in this species to group lines in terms of origin and lines with incomplete origin data. They can also be useful in maize in predicting the hybrid formula and can find applications in the selection of parental components for heterosis crossings.

Genome-wide association mapping reveals putative candidate genes for drought tolerance in barley

2020 ◽  
Vol 180 ◽  
pp. 104237
Author(s):  
Rasha A. Tarawneh ◽  
Ahmad M. Alqudah ◽  
Manuela Nagel ◽  
Andreas Börner
Keyword(s):  
Drought Tolerance ◽  
Association Mapping ◽  
Candidate Genes ◽  
Genome Wide Association ◽  
Genome Wide

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

2020 ◽  
Vol 126 (7) ◽  
pp. 1193-1202 ◽  
Author(s):  
Sarin Neang ◽  
Marjorie de Ocampo ◽  
James A Egdane ◽  
John Damien Platten ◽  
Abdelbagi M Ismail ◽  
...  
Keyword(s):  
Salt Stress ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Leaf Sheath ◽  
Salt Transport ◽  
Nucleotide Polymorphisms ◽  
Rice Varieties ◽  
Gwas Study ◽  
A Genome

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.

scholarly journals Association Mapping for Drought Tolerance and Yield-Related Traits in Cowpea Accessions

2020 ◽  
Author(s):  
Gabriel Vusanimuzi Nkomo ◽  
Moosa Sedibe ◽  
Maletsema Alina Mofokeng ◽  
Rian Pierneef
Keyword(s):  
Drought Tolerance ◽  
Association Mapping ◽  
Linear Model ◽  
Genotyping By Sequencing ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Single Marker ◽  
Peak Of Delta

The objective of this study were to conduct association mapping for drought tolerance at the seedling stage and yield-related traits. 60 cowpea accessions were used in the study. Single-nucleotide polymorphisms (SNPs) discovered through genotyping by sequencing (GBS) were used for genotyping. Association mapping was conducted using single-marker regression (SMR) in Q Gene, and general linear model (GLM) and mixed linear model (MLM) built in TASSEL. The population of the cowpea accessions were analysed using STRUCTURE 2.3.4 and the peak of delta K in the greenhouse showed seven population types, whereas the peak of delta K in the glasshouse indicated the presence of six population types. One SNP marker, 14083649|F|0-9 was associated with NP with a p value &lt;0.001. Fifty SNP markers were associated with PWT at p &lt;0.001. Four SNP markers, 14074781|F|0-16, 100047392|F|0-36, 14083801|F|0-28 and 100051488|F|0-49 were associated with AVSPD at p &lt;0.001. SNP markers, 14074781|F|0-16, 14083801|F|0-28 and 100051488|F|0-49 were associated with PL at P &lt;0.001. Five SNP markers, 100047392|F|0-36, 14083801|F|0-28, 100072738|F|0-34, 14076881|F|0-49 and 14076881|F|0-49 were associated with PWDTH at p &lt;0.001. The 65 SNP markers identified can be used in cowpea molecular breeding to select for AVSPD, NP, PL, PWDTH, PWT, and RR through marker assisted selection (MAS).

Does basic education students know the importance of agroecology production systems for the conservation of biodiversity?

2020 ◽  
Vol 9 (4) ◽  
pp. e04942784
Author(s):  
Andrea Aline Mombach ◽  
Carla Grasiele Zanin Hegel ◽  
Rogério Luis Cansian ◽  
Sônia Beatris Balvedi Zakrzevski
Keyword(s):  
Student Perceptions ◽  
Rural Areas ◽  
Water Conservation ◽  
Social Transformation ◽  
Basic Education ◽  
Production Systems ◽  
Agricultural Systems ◽  
Education Students ◽  
Chi Square ◽  
Conservation Of Biodiversity

The perception of a basic education of the importance of agroecological agricultural systems for human and environmental health is fundamental for changes in consumption habits, the conservation of local biodiversity and long-term social transformation. We analyzed, by utilizing a questionnaire consisting of open and closed questions, the perceptions about agroecological and conventional agricultural production systems in 360 final students of basic education residing in nine Functional Planning Regions of southern Brazil. We used classification categories for answers within thematic axes, expressed in percentages and analyzed by means of Chi-square and Kruskal-Wallis tests. In general, students recognize agroecological systems as healthier for their families and for soil and water conservation, largely because they do not use agrochemicals. However, they demonstrated difficulties when arguing their importance for the conservation of biodiversity, ecosystems and for ensuring the food security of populations. Television was the main source of information related to agroecology, mainly for students residing in rural areas, thus pointing out shortcomings in basic education regarding the approach of the theme in schools. Our results show the need to build a complex network of knowledge and discussions on agroecological agricultural systems in basic education, involving changes in student perceptions, behaviors and sustainable choices.

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