scholarly journals Identification of a Saltol-independent Salinity Tolerance Polymorphism in Rice Mekong Delta Landraces and Characterization of a Promising Line, Doc Phung

2021 ◽  
Author(s):  
Nguyen Thanh Tam ◽  
Maria Stefanie Dwiyanti ◽  
Shuntaro Sakaguchi ◽  
Yohei Koide ◽  
Le Viet Dung ◽  
...  
Keyword(s):  
Salinity Tolerance ◽  
Evaluation System ◽  
Association Studies ◽  
Mekong Delta ◽  
Dry Weight ◽  
Shoot Elongation ◽  
Wide Distribution ◽  
Chromosome 1 ◽  
Genome Wide Association Studies ◽  
Shoot Dry Weight

Abstract The Mekong Delta River in Vietnam is facing salinity intrusion caused by climate change and sea-level rise that is severely affecting rice cultivation. Here, we evaluated salinity responses of 97 rice accessions (79 landraces and 18 improved accessions) from the Mekong Delta population by adding 100 mM NaCl to the nutrient solution for up to 20 days. We observed a wide distribution in salinity tolerance/sensitivity, with two major peaks across the 97 accessions when using the standard evaluation system (SES) developed by the International Rice Research Institute. SES scores revealed strong negative correlations (ranging from –0.68 to –0.83) with other phenotypic indices, such as shoot elongation length, root elongation length, shoot dry weight, and root dry weight. Mineral concentrations of Na+ in roots, stems, and leaves and Ca2+ in roots and stems were positively correlated with SES scores, suggesting that tolerant accessions lower their cation exchange capacity (CEC) in the root cell wall. The salinity tolerance of Mekong Delta accessions was independent from the previously described salinity tolerance–related locus Saltol, which encodes an HKT1-type transporter in the salinity-tolerant cultivars Nona Bokra and Pokkali. Indeed, genome-wide association studies (GWASs) using SES scores and shoot dry weight ratios of the 79 accessions as traits identified a single common peak located on chromosome 1. This SNP did not form a linkage group with other nearby SNPs and mapped to the 3′ untranslated region of gene LOC_Os01g32830, over 6.5 Mb away from the Saltol locus. LOC_Os01g32830 encodes chloroplast glycolate/glycerate translocator 1 (OsPLGG1), which is responsible for photorespiration and growth. SES and shoot dry weight ratios differed significantly between the two possible haplotypes at the causal SNP. Through these analyses, we characterize Doc Phung, one of the most salt-tolerant varieties in the Mekong Delta population and a promising new genetic resource.

Effect of Herbicides on Germination and Growth of Four Grass Weeds

Weed Science ◽  
1984 ◽  
Vol 32 (4) ◽  
pp. 489-493 ◽  
Author(s):  
Frank L. Young ◽  
David R. Gealy ◽  
Larry A. Morrow
Keyword(s):  
Bromus Tectorum ◽  
Soil Surface ◽  
Dry Weight ◽  
Shoot Elongation ◽  
Downy Brome ◽  
Aegilops Cylindrica ◽  
Shoot Height ◽  
Shoot Dry Weight ◽  
Jointed Goatgrass ◽  
Germination And Growth

In the greenhouse, glyphosate [N-(phosphonomethyl)glycine] at 0.6 kg ae/ha applied directly to seeds alone or seeds on the soil surface reduced germination and shoot dry weight of common rye (Secale cerealeL. ♯3SECCE). Paraquat (1,1′-dimethyl-4,4′-bipyridinium ion) applied similarly at 0.6 kg ai/ha reduced germination and shoot dry weight of downy brome (Bromus tectorumL. ♯ BROTE) and wheat (Triticum aestivumL. ‘Daws' ♯ TRZAX). Metribuzin [4-amino-6-tert-butyl-3-(methylthio)-as-triazin-5 (4H)-one] at 0.6 kg ai/ha applied to seeds, soil, or seeds and soil had very little effect on germination, but significantly reduced shoot dry weight of common rye, downy brome, wheat, and jointed goatgrass (Aegilops cylindricaHost. ♯ AEGCY). Pronamide [3,5-dichloro(N-1,1-dimethyl-2-propynyl)benzamide] at 0.6 kg ai/ha, and propham (isopropyl carbanilate) at 3.4 kg ai/ha plus extender (p-chlorophenyl-N-methylcarbamate) at 0.4 kg ai/ha substantially reduced shoot height and dry weight of all species, regardless of application method, with pronamide completely inhibiting shoot elongation and dry-weight production in three of the four species.

scholarly journals Assembly of chromosome-scale and allele-aware autotetraploid genome of the Chinese alfalfa cultivar Zhongmu-4 and identification of SNP loci associated with 27 agronomic traits

2021 ◽  
Author(s):  
Ruicai Long ◽  
Fan Zhang ◽  
Zhiwu Zhang ◽  
Mingna Li ◽  
Lin Chen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Agronomic Traits ◽  
Association Studies ◽  
Genetic Research ◽  
Chromosome 1 ◽  
Genome Wide Association Studies ◽  
Forage Crops ◽  
Legume Crop ◽  
Population Structure Analysis

AbstractAlfalfa (Medicago sativaL.), the most valuable perennial legume crop, referred to as “Queen of the Forages” for its high nutritional value and yield production among forage crops. Comprehensive genomic information of germplasm resources from different ecological regions and modern breeding strategies, such as molecular-marker assisted breeding are of great importance to breed new alfalfa varieties with environmental resilience. Here, we report assembly of the genome sequence of Zhongmu-4 (ZM-4), one of the most planted cultivars in China, and identification of SNPs associated with alfalfa agronomic traits by Genome-wide Association Studies (GWAS). Sequence of 32 allelic chromosomes was assembled successfully by single molecule real time sequencing and Hi-C technique with ALLHiC algorithm. About 2.74 Gbp contigs, accounting for 88.39% of the estimated genome, were assembled with 2.56 Gbp contigs anchored to 32 pseudo-chromosomes. In comparison withM. truncatulaA17, distinctive inversion and translocation on chromosome 1, and between chromosome 4 and 8, respectively, were detected. Moreover, we conducted resequencing of 220 alfalfa accessions collected globally and performed GWAS analysis based on our assembled genome. Population structure analysis demonstrated that alfalfa has a complex genetic relationship among germplasm with different geographic origins. GWAS identified 101 SNPs associated with 27 out of 93 agronomic traits. The updated chromosome-scale and allele-aware genome sequence, coupled with the resequencing data of most global alfalfa germplasm, provides valuable information for alfalfa genetic research, and further analysis of major SNP loci will accelerate unravelling the molecular basis of important agronomic traits and facilitate genetic improvement of alfalfa.

scholarly journals Detecting Salt Tolerance in Doubled Haploid Wheat Lines

Agronomy ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 211 ◽  
Author(s):  
Al-Ashkar ◽  
Alderfasi ◽  
El-Hendawy ◽  
Al-Suhaibani ◽  
El-Kafafi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Salt Tolerance ◽  
Salinity Tolerance ◽  
Doubled Haploid ◽  
Dry Weight ◽  
Shoot Length ◽  
Salt Tolerant ◽  
Breeding Programs ◽  
Shoot Dry Weight ◽  
Wheat Lines

Improving salt tolerance of genotypes requires a source of genetic variation and multiple accurate selection criteria for discriminating their salt tolerance. A combination of morpho-physiological and biochemical parameters and multivariate analysis was used to detect salt tolerance variation in 15 wheat lines developed by doubled haploid (DHL) technique. They were then compared with the salt-tolerant check cultivar Sakha 93. Salinity stress was investigated at three salinity levels (0, 100, and 200 mM NaCl) for 25 days. Considerable genetic variation was observed for all traits, as was high heritability (>60%) and genetic gain (>20%). Principal component analysis indicated the ability of nine traits (root number, root length, root dry weight, shoot length, shoot dry weight, specific root length, relative water content, membrane stability index, and catalase) to identify differences in salinity tolerance among lines. Three traits (shoot length, shoot dry weight, and catalase) were indicative of salt-tolerance, indicating their importance in improving and evaluating salt tolerant genotypes for breeding programs. The salinity tolerance membership index based on these three traits classified one new line (DHL21) and the check cultivar (Sakha 93) as highly salt-tolerant, DHL25, DHL26, DHL2, DHL11, and DHL5 as tolerant, and DHL23 and DHL12 as intermediate. Discriminant function analysis and MANOVA suggested differences among the five groups of tolerance. Among the donor genotypes, Sakha 93 remained the donor of choice for improving salinity tolerance during the seedling stage. The tolerated lines (DHL21, DHL25, DHL26, DHL2, DHL11, and DHL5) could be also recommended as useful and novel genetic resources for improving salinity tolerance of wheat in breeding programs.

Shoot phenology and water relations of Piceaglauca

1989 ◽  
Vol 19 (10) ◽  
pp. 1287-1290 ◽  
Author(s):  
Steven C. Grossnickle
Keyword(s):  
Osmotic Potential ◽  
Dry Weight ◽  
Shoot Elongation ◽  
Water Relation ◽  
Day Length ◽  
Late Winter ◽  
Turgor Loss Point ◽  
Shoot Dry Weight ◽  
Length Changes ◽  
Shoot Phenology

Piceaglauca var. albertiana (S. Brown) Sarg. shoot phenology and water relation parameters were monitored monthly for 1 year. Seedlings were kept outdoors, well watered, and exposed to seasonal changes in temperature and day length. Changes in shoot water relation parameters corresponded with changes in phenology. During spring, shoot elongation, osmotic potential at saturation, and turgor loss point were least negative, −1.30 and −1.56 MPa, respectively, whereas bulk modulus of elasticity at full turgor was at its highest, 22 MPa. Both osmotic potential at saturation and turgor loss point were most negative, −2.01 and −2.73 MPa, respectively, during late winter just before bud break. Shoot dry weight fraction was at its lowest, 0.33 g dry wt./g shoot weight and maximum symplastic water per unit weight of shoot tissue was at its highest, 3.99 g H2O/g dry wt., during spring shoot elongation. Number of osmoles of solute per kilogram shoot dry weight was highest during spring and late summer shoot elongation phases, 1.03 and 0.91 osmol/kg dry wt., respectively. These data suggest that P. glauca seedlings do not adjust well to dry site conditions.

scholarly journals Genome-Wide Association Study Reveals Key Genes for Differential Lead Accumulation and Tolerance in Natural Arabidopsis thaliana Accessions

2021 ◽  
Vol 12 ◽  
Author(s):  
Sílvia Busoms ◽  
Laura Pérez-Martín ◽  
Miquel Llimós ◽  
Charlotte Poschenrieder ◽  
Soledad Martos
Keyword(s):  
Arabidopsis Thaliana ◽  
Cell Walls ◽  
Association Studies ◽  
Root Cell ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Pb Accumulation ◽  
Root Cell Walls

Soil contamination by lead (Pb) has become one of the major ecological threats to the environment. Understanding the mechanisms of Pb transport and deposition in plants is of great importance to achieve a global Pb reduction. We exposed a collection of 360 Arabidopsis thaliana natural accessions to a Pb-polluted soil. Germination rates, growth, and leaf Pb concentrations showed extensive variation among accessions. These phenotypic data were subjected to genome wide association studies (GWAs) and we found a significant association on chromosome 1 for low leaf Pb accumulation. Genes associated with significant SNP markers were evaluated and we selected EXTENSIN18 (EXT18) and TLC (TRAM-LAG1-CLN8) as candidates for having a role in Pb homeostasis. Six Pb-tolerant accessions, three of them exhibiting low leaf Pb content, and three of them with high leaf Pb content; two Pb-sensitive accessions; two knockout T-DNA lines of GWAs candidate genes (ext18, tlc); and Col-0 were screened under control and high-Pb conditions. The relative expression of EXT18, TLC, and other genes described for being involved in Pb tolerance was also evaluated. Analysis of Darwinian fitness, root and leaf ionome, and TEM images revealed that Pb-tolerant accessions employ two opposing strategies: (1) low translocation of Pb and its accumulation into root cell walls and vacuoles, or (2) high translocation of Pb and its efflux to inactive organelles or intracellular spaces. Plants using the first strategy exhibited higher expression of EXT18 and HMA3, thicker root cell walls and Pb vacuolar sequestration, suggesting that these genes may contribute to the deposition of Pb in the roots. On the other hand, plants translocating high amounts of Pb showed upregulation of TLC and ABC transporters, indicating that these plants were able to properly efflux Pb in the aerial tissues. We conclude that EXT18 and TLC upregulation enhances Pb tolerance promoting its sequestration: EXT18 favors the thickening of the cell walls improving Pb accumulation in roots and decreasing its toxicity, while TLC facilitates the formation of dictyosome vesicles and the Pb encapsulation in leaves. These findings are relevant for the design of phytoremediation strategies and environment restoration.

scholarly journals Controlling Vegetative Growth and Flowering of Four Azalea Cultivars with Uniconazole and GA

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 854C-854
Author(s):  
Ursula K. Schuch ◽  
Barbara Biernacka
Keyword(s):  
Leaf Area ◽  
Plant Height ◽  
Vegetative Growth ◽  
Foliar Spray ◽  
Dry Weight ◽  
Shoot Elongation ◽  
Final Evaluation ◽  
Flower Buds ◽  
Shoot Dry Weight ◽  
Treatment Application

Four azalea cultivars [Rhododendron × `White Lace' (WT), `Southern Charm' (SC), `Formosa' (F), and `George Tabor' (GT)] with different growth and flowering habits were treated with a foliar spray of uniconazole (U) at 0, 10, or 15 mg·liter–1 with or without a surfactant. GA was applied at 0 or 15 mg·liter–1 as a foliar spray to half of the plants on 23 Sept. 1993, 53 days after the uniconazole application. U reduced number, length, and dry weight of bypass shoots, and increased number of flower buds for all cultivars by Dec. 1993. Application of GA after U further increased the number of flower buds on SC and GT, which otherwise had few flowers. At the final evaluation in Mar. 1994, time to anthesis for cultivars F and GT was not affected by any treatment. Anthesis of SC and WL treated with 15 mg U and GA/liter started 6 days earlier than those treated with 15 mg U/liter. Number of flowers at anthesis and number of flower buds was increased two to four times on U-treated vs. nontreated plants. U decreased plant height, size, leaf area, and shoot dry weight of all cultivars. Shoot elongation of F and GT was further reduced with the 15 vs. 10 mg U/liter treatment. Application of GA increased the retarding effects of U on plant height for WL, SC, and GT, and on leaf area and shoot dry weight for WL.

scholarly journals Genome-wide association of phenotypes based on clustering patterns of hand osteoarthritis identify WNT9A as novel osteoarthritis gene

2020 ◽  
pp. annrheumdis-2020-217834
Author(s):  
Cindy Germaine Boer ◽  
Michelle S Yau ◽  
Sarah J Rice ◽  
Rodrigo Coutinho de Almeida ◽  
Kathleen Cheung ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Association Studies ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Hand Osteoarthritis ◽  
Genome Wide Association Studies ◽  
Causal Gene ◽  
Genetic Loci ◽  
Genome Wide ◽  
Clustering Patterns

BackgroundDespite recent advances in the understanding of the genetic architecture of osteoarthritis (OA), only two genetic loci have been identified for OA of the hand, in part explained by the complexity of the different hand joints and heterogeneity of OA pathology.MethodsWe used data from the Rotterdam Study (RSI, RSII and RSIII) to create three hand OA phenotypes based on clustering patterns of radiographic OA severity to increase power in our modest discovery genome-wide association studies in the RS (n=8700), and sought replication in an independent cohort, the Framingham Heart Study (n=1203). We used multiple approaches that leverage different levels of information and functional data to further investigate the underlying biological mechanisms and candidate genes for replicated loci. We also attempted to replicate known OA loci at other joint sites, including the hips and knees.ResultsWe found two novel genome-wide significant loci for OA in the thumb joints. We identified WNT9A as a possible novel causal gene involved in OA pathogenesis. Furthermore, several previously identified genetic loci for OA seem to confer risk for OA across multiple joints: TGFa, RUNX2, COL27A1, ASTN2, IL11 and GDF5 loci.ConclusionsWe identified a robust novel genetic locus for hand OA on chromosome 1, of which WNT9A is the most likely causal gene. In addition, multiple genetic loci were identified to be associated with OA across multiple joints. Our study confirms the potential for novel insight into the genetic architecture of OA by using biologically meaningful stratified phenotypes.

scholarly journals Genetic Regulation of Biomarkers as Stress Proxies in Dairy Cows

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 534
Author(s):  
Marco Milanesi ◽  
Matilde Maria Passamonti ◽  
Katia Cappelli ◽  
Andrea Minuti ◽  
Valentino Palombo ◽  
...  
Keyword(s):  
Inflammatory Responses ◽  
Bos Taurus ◽  
Association Studies ◽  
Meta Analysis ◽  
Genetic Regulation ◽  
Chromosome 1 ◽  
Genome Wide Association Studies ◽  
Genetic Associations ◽  
Physiological Level ◽  
Glutamyl Transferase

Stress in livestock reduces productivity and is a welfare concern. At a physiological level, stress is associated with the activation of inflammatory responses and increased levels of harmful reactive oxygen species. Biomarkers that are indicative of stress could facilitate the identification of more stress-resilient animals. We examined twenty-one metabolic, immune response, and liver function biomarkers that have been associated with stress in 416 Italian Simmental and 436 Italian Holstein cows which were genotyped for 150K SNPs. Single-SNP and haplotype-based genome-wide association studies were carried out to assess whether the variation in the levels in these biomarkers is under genetic control and to identify the genomic loci involved. Significant associations were found for the plasma levels of ceruloplasmin (Bos taurus chromosome 1—BTA1), paraoxonase (BTA4) and γ-glutamyl transferase (BTA17) in the individual breed analysis that coincided with the position of the genes coding for these proteins, suggesting that their expression is under cis-regulation. A meta-analysis of both breeds identified additional significant associations with paraoxonase on BTA 16 and 26. Finding genetic associations with variations in the levels of these biomarkers suggests that the selection for high or low levels of expression could be achieved rapidly. Whether the level of expression of the biomarkers correlates with the response to stressful situations has yet to be determined.

scholarly journals Genome-Wide Association Mapping of Seedling Biomass and Root Traits Under Different Water Conditions in Wheat

2021 ◽  
Vol 12 ◽  
Author(s):  
Iza Fatima ◽  
Yutian Gao ◽  
Xiangru Xu ◽  
Jingjing Jin ◽  
Shuonan Duan ◽  
...  
Keyword(s):  
Association Studies ◽  
Root Traits ◽  
Dry Weight ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Fresh Weight ◽  
Wheat Seedlings ◽  
Genome Wide ◽  
Seedling Biomass ◽  
Water Conditions

Drought is a major threat to global wheat production. In this study, an association panel containing 200 Chinese wheat germplasms was used for genome-wide association studies (GWASs) of genetic loci associated with eight root and seedling biomass traits under normal water and osmotic stress conditions. The following traits were investigated in wheat seedlings at the four-leaf stage: root length (RL), root number (RN), root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW), total fresh weight (TFW), and total dry weight (TDW). A total of 323 and 286 SNPs were detected under two water environments, respectively. Some of these SNPs were near known loci for root traits. Eleven SNPs on chromosomes 1B, 2B, 4B, and 2D had pleiotropic effects on multiple traits under different water conditions. Further analysis indicated that several genes located inside the 4 Mb LD block on each side of these 11 SNPs were known to be associated with plant growth and development and thus may be candidate genes for these loci. Results from this study increased our understanding of the genetic architecture of root and seedling biomass traits under different water conditions and will facilitate the development of varieties with better drought tolerance.

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