scholarly journals Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom®CicerSNP Array in Chickpea

2020 ◽  
Vol 21 (14) ◽  
pp. 5058 ◽  
Author(s):  
Khela Ram Soren ◽  
Praveen Madugula ◽  
Neeraj Kumar ◽  
Rutwik Barmukh ◽  
Meenu Singh Sengar ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Salinity Stress ◽  
Salinity Tolerance ◽  
Snp Markers ◽  
Yield Component ◽  
Phenotypic Variance ◽  
Genetic Dissection ◽  
Major Qtls ◽  
Calcium Dependent ◽  
Yield Component Traits

Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.

Linking osmotic adjustment and stomatal characteristics with salinity stress tolerance in contrasting barley accessions

2015 ◽  
Vol 42 (3) ◽  
pp. 252 ◽  
Author(s):  
Min Zhu ◽  
Meixue Zhou ◽  
Lana Shabala ◽  
Sergey Shabala
Keyword(s):  
Stress Tolerance ◽  
Salinity Stress ◽  
Salinity Tolerance ◽  
Osmotic Adjustment ◽  
Inorganic Ions ◽  
Plant Performance ◽  
Hordeum Vulgare L ◽  
Stomatal Characteristics ◽  
Stomata Density ◽  
Salinity Stress Tolerance

Salinity tolerance is a complex trait – both physiologically and genetically – and the issue of which mechanism or trait has bigger contribution towards the overall plant performance is still hotly discussed in the literature. In this work, a broad range of barley (Hordeum vulgare L. and Hordeum spontaneum L.) genotypes contrasting in salinity stress tolerance were used to investigate the causal link between plant stomatal characteristics, tissue ion relations, and salinity tolerance. In total, 46 genotypes (including two wild barleys) were grown under glasshouse conditions and exposed to moderate salinity stress (200mM NaCl) for 5 weeks. The overall salinity tolerance correlated positively with stomata density, leaf K+ concentration and the relative contribution of inorganic ions towards osmotic adjustment in the shoot. At the same time, no correlation between salinity tolerance and stomatal conductance or leaf Na+ content in the shoot was found. Taken together, these results indicate the importance of increasing stomata density as an adaptive tool to optimise efficiency of CO2 assimilation under moderate saline conditions, as well as benefits of the predominant use of inorganic osmolytes for osmotic adjustment in barley. Another finding of note was that wild barleys showed rather different strategies dealing with salinity, as compared with cultivated varieties.

scholarly journals Novel Salinity Tolerance Loci in Chickpea Identified in Glasshouse and Field Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Judith Atieno ◽  
Timothy D. Colmer ◽  
Julian Taylor ◽  
Yongle Li ◽  
John Quealy ◽  
...  
Keyword(s):  
Salinity Tolerance ◽  
Positional Cloning ◽  
Snp Markers ◽  
Yield Component ◽  
Yield Potential ◽  
Distinct Region ◽  
Salinity Treatment ◽  
Salt Tolerant ◽  
Best Linear Unbiased ◽  
Per Se

A better understanding of the genetics of salinity tolerance in chickpea would enable breeding of salt tolerant varieties, offering potential to expand chickpea production to marginal, salinity-affected areas. A Recombinant Inbred Line population was developed using accelerated-Single Seed Descent of progeny from a cross between two chickpea varieties, Rupali (salt-sensitive) and Genesis836 (salt-tolerant). The population was screened for salinity tolerance using high-throughput image-based phenotyping in the glasshouse, in hydroponics, and across 2 years of field trials at Merredin, Western Australia. A genetic map was constructed from 628 unique in-silico DArT and SNP markers, spanning 963.5 cM. Markers linked to two flowering loci identified on linkage groups CaLG03 and CaLG05 were used as cofactors during genetic analysis to remove the confounding effects of flowering on salinity response. Forty-two QTL were linked to growth rate, yield, and yield component traits under both control and saline conditions, and leaf tissue ion accumulation under salt stress. Residuals from regressions fitting best linear unbiased predictions from saline conditions onto best linear unbiased predictions from control conditions provided a measure of salinity tolerance per se, independent of yield potential. Six QTL on CaLG04, CaLG05, and CaLG06 were associated with tolerance per se. In total, 21 QTL mapped to two distinct regions on CaLG04. The first distinct region controlled the number of filled pods, leaf necrosis, seed number, and seed yield specifically under salinity, and co-located with four QTL linked to salt tolerance per se. The second distinct region controlled 100-seed weight and growth-related traits, independent of salinity treatment. Positional cloning of the salinity tolerance-specific loci on CaLG04, CaLG05, and CaLG06 will improve our understanding of the key determinants of salinity tolerance in chickpea.

scholarly journals DEVELOPMENT AND APPLICATION OF 1536-PLEX SINGLE NUCLEOTIDE POLYMORPHISM MARKER CHIP FOR GENOME WIDE SCANNING OF INDONESIAN RICE GERMPLASM

2013 ◽  
Vol 14 (2) ◽  
pp. 71
Author(s):  
Dwinita W. Utami ◽  
I. Rosdianti ◽  
P. Lestari ◽  
D. Satyawan ◽  
H. Rijzaani ◽  
...  
Keyword(s):  
Molecular Breeding ◽  
Rice Genome ◽  
Heading Date ◽  
Snp Markers ◽  
Yield Component ◽  
Diversity Analysis ◽  
Rice Germplasm ◽  
Genome Wide ◽  
Component Traits ◽  
Yield Component Traits

A successful molecular breeding program requires detailed and comprehensive understanding of the diversity of rice germ-plasm and genetic base of target traits. The objective of this research was to develop the high throughput 1536-SNP chip linked to heading date and yield component traits and used it for genotyping the diverse Indonesian rice germplasm. The genotype data obtained could be used for diversity analysis and genome wide association mapping study. A 1536-SNP genome wide assay was developed using the Illumina’s GoldenGate technology. The SNP markers were selected in the rice genome regions containing heading date and yield component genes or regions where the quantitative trait loci (QTLs) of the two traits were mapped. The developed custom SNP chips were then used for genotyping 467 rice accessions showing diversity in heading dates and yield components. The assay can reliably be used for diversity analysis and mapping genes associated with heading date and yield component traits. For 1536-SNP BIO-RiceOPA-1 custom chip designed, a total of 34.832 SNPs distributed in rice genome particularly in the region of heading date and yield component genes or QTLs were identified. A total of 1536-SNP were selected and confirmed to be used for genotyping analysis. Analysis performance and quality of 1536-SNP BIO-RiceOPA1 showed that 60% (918/1536) of total SNP markers had a good differentiating power in scanning the rice accessions tested (MAF &gt; 0.2). The 1536-SNP genome wide assay Illumina’s GoldenGate designed was useful for diversity analysis and could be used as SNP marker for large scale genotyping in rice molecular breeding involving Indica-Indica, Indica-Japonica and Indica-Tropical Japonica crosses. <br />

scholarly journals GABA operates upstream of H+-ATPase and improves salinity tolerance in Arabidopsis by enabling cytosolic K+ retention and Na+ exclusion

2019 ◽  
Vol 70 (21) ◽  
pp. 6349-6361 ◽  
Author(s):  
Nana Su ◽  
Qi Wu ◽  
Jiahui Chen ◽  
Lana Shabala ◽  
Axel Mithöfer ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Salinity Stress ◽  
Salinity Tolerance ◽  
Plant Roots ◽  
Transcript Levels ◽  
Root Epidermis ◽  
Beneficial Effects ◽  
Salinity Stress Tolerance ◽  
Increased Activity

GABA has beneficial effects on salinity stress tolerance in Arabidopsis linked to increased activity of H+-ATPase, reduced ROS-induced K+ efflux from root epidermis, and increased SOS1 and NHX1 transcript levels in plant roots.

scholarly journals Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.)

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1402
Author(s):  
Mounirou Hachim Alyr ◽  
Justine Pallu ◽  
Aissatou Sambou ◽  
Joel Romaric Nguepjop ◽  
Maguette Seye ◽  
...  
Keyword(s):  
Seed Size ◽  
Genomic Region ◽  
Snp Markers ◽  
Yield Component ◽  
Proximal Region ◽  
Chromosome Segment ◽  
Single Marker Analysis ◽  
Advanced Backcross ◽  
F2 Population ◽  
Yield Component Traits

Fruit and seed size are important yield component traits that have been selected during crop domestication. In previous studies, Advanced Backcross Quantitative Trait Loci (AB-QTL) and Chromosome Segment Substitution Line (CSSL) populations were developed in peanut by crossing the cultivated variety Fleur11 and a synthetic wild allotetraploid (Arachis ipaensis × Arachis duranensis)4x. In the AB-QTL population, a major QTL for pod and seed size was detected in a ~5 Mb interval in the proximal region of chromosome A07. In the CSSL population, the line 12CS_091, which carries the QTL region and that produces smaller pods and seeds than Fleur11, was identified. In this study, we used a two-step strategy to fine-map the seed size QTL region on chromosome A07. We developed new SSR and SNP markers, as well as near-isogenic lines (NILs) in the target QTL region. We first located the QTL in ~1 Mb region between two SSR markers, thanks to the genotyping of a large F2 population of 2172 individuals and a single marker analysis approach. We then used nine new SNP markers evenly distributed in the refined QTL region to genotype 490 F3 plants derived from 88 F2, and we selected 10 NILs. The phenotyping of the NILs and marker/trait association allowed us to narrowing down the QTL region to a 168.37 kb chromosome segment, between the SNPs Aradu_A07_1148327 and Aradu_A07_1316694. This region contains 22 predicted genes. Among these genes, Aradu.DN3DB and Aradu.RLZ61, which encode a transcriptional regulator STERILE APETALA-like (SAP) and an F-box SNEEZY (SNE), respectively, were of particular interest. The function of these genes in regulating the variation of fruit and seed size is discussed. This study will contribute to a better knowledge of genes that have been targeted during peanut domestication.

scholarly journals Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1088
Author(s):  
Thao Duc Le ◽  
Floran Gathignol ◽  
Huong Thi Vu ◽  
Khanh Le Nguyen ◽  
Linh Hien Tran ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Salinity Stress ◽  
Salinity Tolerance ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Transport Systems ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Salinity Stress Tolerance

Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K+ and Na+ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice.

scholarly journals Mapping genomic regions of moisture deficit stress tolerance using backcross inbred lines in wheat (Triticum aestivum L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shashikumara Puttamadanayaka ◽  
Harikrishna ◽  
Manu Balaramaiah ◽  
Sunil Biradar ◽  
Sunilkumar V. Parmeshwarappa ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Marker Assisted Selection ◽  
Inbred Lines ◽  
Yield Component ◽  
Backcross Inbred Lines ◽  
Moisture Deficit ◽  
Component Traits ◽  
Yield Component Traits ◽  
Genomic Regions ◽  
Moisture Deficit Stress

AbstractIdentification of markers associated with major physiological and yield component traits under moisture deficit stress conditions in preferred donor lines paves the way for marker-assisted selection (MAS). In the present study, a set of 183 backcross inbred lines (BILs) derived from the cross HD2733/2*C306 were genotyped using 35K Axiom genotyping array and SSR markers. The multi-trait, multi-location field phenotyping of BILs was done at three locations covering two major wheat growing zones of India, north-western plains zone (NWPZ) and central zone (CZ) under varying moisture regimes. A linkage map was constructed using 705 SNPs and 86 SSR polymorphic markers. A total of 43 genomic regions and QTL × QTL epistatic interactions were identified for 14 physiological and yield component traits, including NDVI, chlorophyll content, CT, CL, PH, GWPS, TGW and GY. Chromosomes 2A, 5D, 5A and 4B harbors greater number of QTLs for these traits. Seven Stable QTLs were identified across environment for DH (QDh.iari_6D), GWPS (QGWPS.iari_5B), PH (QPh.iari_4B-2, QPh.iari_4B-3) and NDVI (QNdvi1.iari_5D, QNdvi3.iari_5A). Nine genomic regions identified carrying major QTLs for CL, NDVI, RWC, FLA, PH, TGW and biomass explaining 10.32–28.35% of the phenotypic variance. The co-segregation of QTLs of physiological traits with yield component traits indicate the pleiotropic effects and their usefulness in the breeding programme. Our findings will be useful in dissecting genetic nature and marker-assisted selection for moisture deficit stress tolerance in wheat.

scholarly journals Assessment of Agro-Morphologic Performance, Genetic Parameters and Clustering Pattern of Newly Developed Blast Resistant Rice Lines Tested in Four Environments

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1098 ◽  
Author(s):  
Raieah Saiyedah Sabri ◽  
Mohd Y. Rafii ◽  
Mohd Razi Ismail ◽  
Oladosu Yusuff ◽  
Samuel C. Chukwu ◽  
...  
Keyword(s):  
Analysis Of Variance ◽  
Phenotypic Variability ◽  
Block Design ◽  
Peninsular Malaysia ◽  
Yield Component ◽  
Phenotypic Variance ◽  
Genetic Advance ◽  
Commercial Cultivation ◽  
Days To Maturity ◽  
Yield Component Traits

Multi-environmental yield trial is very vital in assessing newly developed rice lines for its adaptability and stability across environments especially prior to release of the newly developed variety for commercial cultivation. The growth performance and phenotypic variability of these genotypes are the combination of environment, genotype and genotype by environment (G×E) interaction factors. Thus, evaluation creates an opportunity for effective selection of superior genotypes. The objectives of this study were to evaluate the newly developed blast resistant rice lines in varied environmental conditions, precisely measure the response of the advanced lines in multiple environments and classify the genotypes into groups that could serve as varieties for commercial cultivation. Genetic materials included 18 improved blast resistant rice lines and the recipient parent MR219. The total of 19 newly developed genotypes was evaluated under four varied environments in Peninsular Malaysia. The experiments were carried out using randomized complete block design (RCBD) with three replications at each environment. Data were collected on the vegetative, yield and yield component traits. Descriptive statistics (mean performance) and analysis of variance were conducted using SAS Software version 9.4. Genotypic and phenotypic coefficients, phenotypic variance component, heritability and genetic advance were also determined. Analysis of variance revealed that all traits were significantly different for genotypes except days to maturity, number of filled grains and total number of grains. Meanwhile, all the traits differed significantly for genotype × environment (G×E) except number of tillers per hill and number of panicles per hill. Low heritability (<30%) was found for all the traits. Similarly, low genetic advance was also observed for all the traits except for number of tillers per hill and number of panicles per hill. yield per hectare had significant and positive correlation with most evaluated traits except for days to flowering, days to maturity, plant height and number of unfilled grains. Cluster analysis classified the 19 evaluated genotypes into six groups. Therefore, the six clusters/groups of genotypes were recommended as varieties for commercial cultivation in Malaysia and other rice growing regions.

scholarly journals DEVELOPMENT AND APPLICATION OF 1536-PLEX SINGLE NUCLEOTIDE POLYMORPHISM MARKER CHIP FOR GENOME WIDE SCANNING OF INDONESIAN RICE GERMPLASM

2013 ◽  
Vol 14 (2) ◽  
pp. 71
Author(s):  
Dwinita W. Utami ◽  
I. Rosdianti ◽  
P. Lestari ◽  
D. Satyawan ◽  
H. Rijzaani ◽  
...  
Keyword(s):  
Molecular Breeding ◽  
Rice Genome ◽  
Heading Date ◽  
Snp Markers ◽  
Yield Component ◽  
Diversity Analysis ◽  
Rice Germplasm ◽  
Genome Wide ◽  
Component Traits ◽  
Yield Component Traits

A successful molecular breeding program requires detailed and comprehensive understanding of the diversity of rice germ-plasm and genetic base of target traits. The objective of this research was to develop the high throughput 1536-SNP chip linked to heading date and yield component traits and used it for genotyping the diverse Indonesian rice germplasm. The genotype data obtained could be used for diversity analysis and genome wide association mapping study. A 1536-SNP genome wide assay was developed using the Illumina’s GoldenGate technology. The SNP markers were selected in the rice genome regions containing heading date and yield component genes or regions where the quantitative trait loci (QTLs) of the two traits were mapped. The developed custom SNP chips were then used for genotyping 467 rice accessions showing diversity in heading dates and yield components. The assay can reliably be used for diversity analysis and mapping genes associated with heading date and yield component traits. For 1536-SNP BIO-RiceOPA-1 custom chip designed, a total of 34.832 SNPs distributed in rice genome particularly in the region of heading date and yield component genes or QTLs were identified. A total of 1536-SNP were selected and confirmed to be used for genotyping analysis. Analysis performance and quality of 1536-SNP BIO-RiceOPA1 showed that 60% (918/1536) of total SNP markers had a good differentiating power in scanning the rice accessions tested (MAF &gt; 0.2). The 1536-SNP genome wide assay Illumina’s GoldenGate designed was useful for diversity analysis and could be used as SNP marker for large scale genotyping in rice molecular breeding involving Indica-Indica, Indica-Japonica and Indica-Tropical Japonica crosses. <br />

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