Genetic Mapping Reveals Novel Exotic and Elite QTL Alleles for Salinity Tolerance in Barley

Soil salinity is one of the constraints of crop production in Egypt. The aims of this study were to identify genomic regions associated with grain weight and its related traits along with their salinity tolerance indices and to identify the most salinity tolerant and high-yielding genotypes. Therefore, we evaluated an advanced backcross mapping population of barley in newly reclaimed soil under two salinity levels of groundwater aquifers in South of Sinai, Egypt. We detected significant QTL associated with grain weight related attributes and the salinity tolerance index (STI) distributed throughout the whole genome of barley, which can be used to enhance salinity tolerance. Moreover, the markers bPb-3739 (4H, 96.3 cM), AF043094A (5H, 156 cM), bPb-8161 (7H, 2.22 cM), and bPb-5260 (7H, 115.6 cM), were the most important identified genomic regions corresponding to vernalization, dwarfing and dehydrin genes, which are correlated with salinity tolerance. Additionally, the doubled haploid lines SI001, SI043, SI044, SI028, SI242, SI035, and SI005 had the highest STI values based on yield average. The present study demonstrated that wild and elite barley do harbor novel valuable alleles, which can enrich the genetic basis of cultivated barley and improve quantitative agronomic traits under salinity conditions.

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Key traits and genes associate with salinity tolerance independent from vigor in cultivated sunflower (Helianthus annuus L.)

10.1101/2020.05.12.090837 ◽

2020 ◽

Cited By ~ 1

Author(s):

Andries A. Temme ◽

Kelly L. Kerr ◽

Rishi R. Masalia ◽

John M. Burke ◽

Lisa A. Donovan

Keyword(s):

Salinity Tolerance ◽

Mass Fraction ◽

Crop Production ◽

Association Studies ◽

Single Gene ◽

Genome Wide Association Studies ◽

Root Mass ◽

Trade Off ◽

High Performing ◽

Genomic Regions

AbstractWith rising food demands, crop production on salinized lands is increasingly necessary. Sunflower, a moderately salt tolerant crop, exhibits a trade-off where more vigorous, high-performing genotypes have a greater proportional decline in biomass under salinity stress. Prior research has found deviations from this relationship across genotypes; the magnitude and direction of these deviations provides a useful metric of tolerance. Here, we identified the traits and genomic regions underlying variation in this expectation-deviation tolerance. We grew a diversity panel under control and salt-stressed conditions and measured a suite of morphological (growth, allocation, plant and leaf morphology) and leaf ionomic traits. The genetic basis of variation in these traits and their plasticity was investigated via genome-wide association studies, which also enabled the identification of genomic regions (i.e., haplotypic blocks) influencing multiple traits. We found that the magnitude of plasticity in whole root mass fraction, fine root mass fraction, and chlorophyll content, as well as leaf Na and K content under saline conditions, were the traits most strongly correlated with expectation-deviation tolerance. Additionally, we identified multiple genomic regions underlying these traits as well as a single gene directly associated with this tolerance metric. Our results show that, by taking the vigor-salinity effect trade-off into account, we can identify unique traits and genes associated with salinity tolerance. Since these traits and genomic regions are distinct from those associated with high vigor (i.e., growth in benign conditions), they provide an avenue for increasing salinity tolerance in high-performing sunflower genotypes without compromising vigor.Single sentence summaryDespite a trade-off between vigor and salinity-induced decline in biomass, distinct traits and genomic regions exist that could modulate this trade-off in cultivated sunflower.

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Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions

Scientific Reports ◽

10.1038/s41598-021-86259-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bahman Khahani ◽

Elahe Tavakol ◽

Vahid Shariati ◽

Laura Rossini

Keyword(s):

Water Deficit ◽

Root Architecture ◽

Agronomic Traits ◽

Heading Date ◽

Dry Weight ◽

Genetic Dissection ◽

Rice Varieties ◽

Average Confidence ◽

Stable Qtls ◽

Genomic Regions

AbstractMeta-QTL (MQTL) analysis is a robust approach for genetic dissection of complex quantitative traits. Rice varieties adapted to non-flooded cultivation are highly desirable in breeding programs due to the water deficit global problem. In order to identify stable QTLs for major agronomic traits under water deficit conditions, we performed a comprehensive MQTL analysis on 563 QTLs from 67 rice populations published from 2001 to 2019. Yield and yield-related traits including grain weight, heading date, plant height, tiller number as well as root architecture-related traits including root dry weight, root length, root number, root thickness, the ratio of deep rooting and plant water content under water deficit condition were investigated. A total of 61 stable MQTLs over different genetic backgrounds and environments were identified. The average confidence interval of MQTLs was considerably refined compared to the initial QTLs, resulted in the identification of some well-known functionally characterized genes and several putative novel CGs for investigated traits. Ortho-MQTL mining based on genomic collinearity between rice and maize allowed identification of five ortho-MQTLs between these two cereals. The results can help breeders to improve yield under water deficit conditions.

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Fungicide Application Affects Nitrogen Utilization Efficiency, Grain Yield, and Quality of Winter Wheat

Agronomy ◽

10.3390/agronomy11071295 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1295

Author(s):

Ahossi Patrice Koua ◽

Mirza Majid Baig ◽

Benedict Chijioke Oyiga ◽

Jens Léon ◽

Agim Ballvora

Keyword(s):

Synergistic Effect ◽

Grain Yield ◽

Crop Production ◽

Agronomic Traits ◽

Yellow Rust ◽

Wheat Yield ◽

Utilization Efficiency ◽

High Nitrogen ◽

Available N ◽

Fungicide Application

Nitrogen (N) is a vital component of crop production. Wheat yield varies significantly under different soil available N. Knowing how wheat responds to or interacts with N to produce grains is essential in the selection of N use efficient cultivars. We assessed in this study variations among wheat genotypes for productivity-related traits under three cropping systems (CS), high-nitrogen with fungicide (HN-WF), high-nitrogen without fungicide (HN-NF) and low-nitrogen without fungicide (LN-NF) in the 2015, 2016 and 2017 seasons. ANOVA results showed genotypes, CS, and their interactions significantly affected agronomic traits. Grain yield (GY) increased with higher leaf chlorophyll content, importantly under CS without N and fungicide supply. Yellow rust disease reduced the GY by 20% and 28% in 2015 and 2016, respectively. Moreover, averaged over growing seasons, GY was increased by 23.78% under CS with N supply, while it was greatly increased, by 52.84%, under CS with both N and fungicide application, indicating a synergistic effect of N and fungicide on GY. Fungicide supply greatly improved the crop ability to accumulate N during grain filling, and hence the grain protein content. Recently released cultivars outperformed the older ones in most agronomic traits including GY. Genotype performance and stability analysis for GY production showed differences in their stability levels under the three CS. The synergistic effect of nitrogen and fungicide on grain yield (GY) and the differences in yield stability levels of recently released wheat cultivars across three CS found in this study suggest that resource use efficiency can be improved via cultivar selection for targeted CS.

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Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab024 ◽

2021 ◽

Author(s):

Rajanikanth Govindarajulu ◽

Ashley N Hostetler ◽

Yuguo Xiao ◽

Srinivasa R Chaluvadi ◽

Margarita Mauro-Herrera ◽

...

Keyword(s):

Agronomic Traits ◽

Interspecific Cross ◽

Crop Improvement ◽

Differentially Expressed ◽

Plant Domestication ◽

Sorghum Propinquum ◽

Ril Population ◽

Trait Locus ◽

Genomic Regions ◽

Low Coverage

Abstract Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.

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Early Growth Stage Characterization and the Biochemical Responses for Salinity Stress in Tomato

Plants ◽

10.3390/plants10040712 ◽

2021 ◽

Vol 10 (4) ◽

pp. 712

Author(s):

Md Sarowar Alam ◽

Mark Tester ◽

Gabriele Fiene ◽

Magdi Ali Ahmed Mousa

Keyword(s):

Salt Tolerance ◽

Salinity Tolerance ◽

Salinity Treatment ◽

Salt Tolerant ◽

Improvement Program ◽

Biochemical Basis ◽

Elevated Salinity ◽

Tolerance Indices ◽

Promising Source ◽

Tomato Genotypes

Salinity is one of the most significant environmental stresses for sustainable crop production in major arable lands of the globe. Thus, we conducted experiments with 27 tomato genotypes to screen for salinity tolerance at seedling stage, which were treated with non-salinized (S1) control (18.2 mM NaCl) and salinized (S2) (200 mM NaCl) irrigation water. In all genotypes, the elevated salinity treatment contributed to a major depression in morphological and physiological characteristics; however, a smaller decrease was found in certain tolerant genotypes. Principal component analyses (PCA) and clustering with percentage reduction in growth parameters and different salt tolerance indices classified the tomato accessions into five key clusters. In particular, the tolerant genotypes were assembled into one cluster. The growth and tolerance indices PCA also showed the order of salt-tolerance of the studied genotypes, where Saniora was the most tolerant genotype and P.Guyu was the most susceptible genotype. To investigate the possible biochemical basis for salt stress tolerance, we further characterized six tomato genotypes with varying levels of salinity tolerance. A higher increase in proline content, and antioxidants activities were observed for the salt-tolerant genotypes in comparison to the susceptible genotypes. Salt-tolerant genotypes identified in this work herald a promising source in the tomato improvement program or for grafting as scions with improved salinity tolerance in tomato.

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Salicylic acid and kaolin effects on pomological, physiological, and phytochemical characters of hazelnut (Corylus avellana) at warm summer condition

Scientific Reports ◽

10.1038/s41598-021-83790-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Marziyeh Khavari ◽

Reza Fatahi ◽

Zabihollah Zamani

Keyword(s):

Salicylic Acid ◽

Crop Production ◽

Corylus Avellana ◽

Kernel Weight ◽

Population Increase ◽

Tolerance Index ◽

Biotic And Abiotic Stresses ◽

The World ◽

Warm Summer ◽

Supporting Materials

AbstractClimate change and population increase are two challenges for crop production in the world. Hazelnut (Corylus avellana L.) is considered an important nut regarding its nutritional and economic values. As a fact, the application of supporting materials as foliage sprays on plants will decrease biotic and abiotic stresses. In this study, the effects of salicylic acid (0, 1 mM and 2.5 mM) and kaolin (0, 3% and 6%) sprays were investigated on morphological, physiological, pomological, and biochemical characteristics of hazelnut. The results showed that 1 mM salicylic acid and 6% kaolin had the best effects on nut and kernel weight compared to control. Biochemical parameters such as chlorophyll a, b, a + b, and carotenoid contents showed that salicylic acid and kaolin improved pigment concentration. Proline and antioxidant contents such as phenolic acids, SOD, APX, and CAT enzyme activities increased by these applications. On the other hand, lipid peroxidation, protein content, and H2O2 content were decreased. Based on the tolerance index result, Merveille de Bollwiller cultivar showed the highest tolerance while 'Fertile de Coutard' had the lowest value. Therefore, hazelnut performance may be improved through exogenous application of the signaling (salicylic acid) and particle film (Kaolin) compounds in warmer climates.

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Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

Rice ◽

10.1186/s12284-020-00433-0 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Leila Nayyeripasand ◽

Ghasem Ali Garoosi ◽

Asadollah Ahmadikhah

Keyword(s):

Association Study ◽

Candidate Gene ◽

Candidate Genes ◽

Salinity Tolerance ◽

Genome Wide Association Study ◽

Dry Weight ◽

Genome Wide Association ◽

Vegetative Stage ◽

Genome Wide ◽

Genomic Regions

Abstract Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. Conclusion Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

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Canaryseed (Phalaris canariensis L.) accessions from nineteen countries show useful genetic variation for agronomic traits

Canadian Journal of Plant Science ◽

10.4141/cjps09200 ◽

2011 ◽

Vol 91 (1) ◽

pp. 37-48 ◽

Cited By ~ 2

Author(s):

M. Cogliatti ◽

F. Bongiorno ◽

H. Dalla Valle ◽

W J Rogers

Keyword(s):

Genetic Variation ◽

Grain Yield ◽

Harvest Index ◽

Agronomic Traits ◽

Grain Weight ◽

Environment Interaction ◽

Grain Number ◽

Harvest Maturity ◽

Phalaris Canariensis ◽

Late Sowing

Fifty-seven accessions of canaryseed (47 populations and 10 cultivars) from 19 countries were evaluated for agronomic traits in four field trials sown over 3 yr in the province of Buenos Aires, Argentina. Genetic variation was found for all traits scored: grain yield and its components (grain weight, grain number per square meter, grain number per head and head number per square meter), harvest index, percent lodging, and phenological characters (emergence to heading, emergence to harvest maturity and heading to harvest maturity). Although genotype × environment interaction was observed for all traits, the additive differences between accessions were sufficient to enable promising breeding materials to be identified. Accessions superior in performance to the local Argentinean population, which in general gave values close to the overall mean of the accessions evaluated, were identified. For example, a population of Moroccan origin gave good yield associated with elevated values of the highly heritable character grain weight, rather than with the more commonly observed grain number per square meter. This population was also of relatively short stature and resistant to lodging, and, although it performed best when sown within the normal sowing date, tolerated late sowing fairly well. Other accessions were also observed with high grain weight, a useful characteristic in itself, since large grains are desirable from a quality point of view. Regarding phenology, the accessions showed a range of 160 degree days (8 calendar days in our conditions) in maturity, which, while not large in magnitude, may be of some utility in crop rotation management. Some accessions were well adapted to late sowing. Grain yield in general was strongly correlated with grain number per square meter. Principal components analysis (PCA) carried out for all characteristics provided indications of accessions combining useful characteristics and identified three components that explained approximately 70% of the phenotypic variation. Furthermore, a second PCA plus regression showed that approximately 60% of the variation in grain yield could be explained by a component associated with harvest index and grain number per square meter. Pointers were provided to possible future breeding targets.Key words: Phalaris canariensis, canaryseed, accessions, yield, phenology, genetics, breeding

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The Use of Germination Indices for Salinity Tolerance Classification of Pepper Cultivars

Turkish Journal of Agriculture - Food Science and Technology ◽

10.24925/turjaf.v7i9.1304-1309.2521 ◽

2019 ◽

Vol 7 (9) ◽

pp. 1304

Author(s):

Gamze Kaya

Keyword(s):

Salinity Tolerance ◽

Seedling Growth ◽

Growth Parameters ◽

Genotypic Variation ◽

Germination Percentage ◽

Control Treatment ◽

Tolerance Index ◽

Seedling Length ◽

Early Seedling ◽

Germination Indices

The study aimed to evaluate the use of germination indices as a screening tool for salinity tolerance during germination and early seedling growth of pepper cultivars, and to distinguish the potential for genetic responses to salt tolerance. In the study, the seeds of seven pepper cultivars were germinated at increasing NaCl levels of 5, 10, 15 and 20 dS/m and distilled water as the control treatment for 14 days. Germination percentage (GP), mean germination time (MGT), germination index (GI), germination stress tolerance index (GSTI), seedling length (SL), seedling fresh weight (SFW) and vigor index (VI) were investigated. Results showed that germination percentage decreased with increasing NaCl levels while the highest germination percentage at 20 dS/m was 92% in BT Burdem with no significant reduction. Seedling growth of pepper cultivars was severely inhibited by increasing salinity stress. SFW was depressed depending on reduction in SL due to increasing NaCl. BT-Burli and BT İnce Sivri were the most tolerant cultivars to NaCl and they were used for genetic resources towards salinity. Seedling growth was much more sensitive to salinity than germination because of the highest percent reduction in seedling growth parameters. Among the parameters, GSTI gave the highest significant correlation coefficient with SL and SFW; indicating that it would be useful for estimating seedling growth. It was concluded that genotypic variation was observed among pepper cultivars for salinity tolerance and GSTI could be used for a predictor for salinity tolerance.

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Discrimination of drought tolerance in a worldwide collection of safflower (Carthamus tinctorius L.) genotypes based on selection indices

Acta agriculturae Slovenica ◽

10.14720/aas.2021.117.1.1656 ◽

2021 ◽

Vol 117 (1) ◽

pp. 1

Author(s):

Pooran GOLKAR ◽

Esmaeil HAMZEH ◽

Seyed Ali Mohammad MIRMOHAMMADY MAIBODY

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Geometric Mean ◽

Resistance Index ◽

Stability Index ◽

Carthamus Tinctorius ◽

Tolerance Index ◽

Breeding Programs ◽

Drought Tolerance Indices ◽

Tolerance Indices

Improvement of elite safflower genotypes for drought-tolerance is hampered by a deficiency of effective selection criteria. The present study evaluated 100 genotypes of safflower in terms of their drought tolerance over a period of three years (2016–2018) under both non-stress and drought-stress conditions. The eight drought-tolerance indices of tolerance index (TOL), mean productivity (MP), geometric mean productivity (GMP), stress susceptibility index (SSI), stress tolerance index (STI), yield stability index (YSI), drought resistance index (DI), and harmonic mean (HARM) were calculated based on seed yield under drought (Ys) and non-drought (Yp) conditions. A high genetic variation was found in drought tolerance among the genotypes studied. The MP, GMP, and STI indices were able to discriminate between tolerant and drought-sensitive genotypes. Plots of the first and second principal components identified drought-tolerant genotypes averaged over the three study years. Cluster analysis divided the genotypes into three distinct groups using the drought tolerance indices. Ultimately, eight genotypes (namely, G3, G11, G13, G24, G33, G47, G58, and G61) from different origins were detected as more tolerant to drought stress suitable for use in safflower breeding programs in drought-affected areas. The most tolerant and susceptible genotypes could be exploited to produce mapping populations for drought tolerance breeding programs in safflower.

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