QTL mapping reveals genomic regions for yield based on incremental tolerance index to drought stress and related agronomic traits in canola

AbstractDrought stress especially at the reproductive stage is a major limiting factor that compromises the productivity and profitability of canola in many regions of the world. Improved genetics for drought tolerance would enable the identification and development of resilient varieties, resulting in increased canola production. The main objective of this study was to dissect the genetic basis of seed yield under water-limited conditions in canola. A doubled haploid population derived from a cross between two Australian parental lines, RP04 and Ag-Outback, was evaluated to identify the genetic variation in fractional normalised deviation vegetative index (NDVI), above ground shoot biomass accumulation, flowering time, and plasticity in seed yield under irrigated and rainfed field conditions in two consecutive years. An irrigation treatment was applied at the 50% flowering stage and an incremental drought tolerance index (DTI) was estimated for seed yield. By utilising a genetic linkage map based on 18,851 genome-wide DArTseq markers, we identified 25 genomic regions significantly associated with different traits (LOD ≥ 3), accounting for 5.5 to 22.3% of the genotypic variance. Three significant genomic regions on chromosome A06, A10 and C04 were associated with DTI for seed yield. Some of the QTL were localised in the close proximity of candidates genes involved in traits contributing to drought escape and drought avoidance mechanisms, including FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC). Trait-marker associations identified herein can be validated across diverse environments, and the sequence based markers may be used in a marker assisted selection breeding strategy to enhance drought tolerance in canola breeding germplasm.

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QTL mapping reveals genomic regions for yield based on an incremental tolerance index to drought stress and related agronomic traits in canola

Crop and Pasture Science ◽

10.1071/cp20046 ◽

2020 ◽

Vol 71 (6) ◽

pp. 562

Author(s):

Harsh Raman ◽

Rosy Raman ◽

Ky Mathews ◽

Simon Diffey ◽

Phil Salisbury

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Seed Yield ◽

Irrigation Treatment ◽

Shoot Biomass ◽

Doubled Haploid Population ◽

Limiting Factor ◽

Tolerance Index ◽

Flowering Locus ◽

Genomic Regions

Drought stress, especially at the reproductive stage, is a major limiting factor that compromises the productivity and profitability of canola in many regions of the world. Improved genetics for drought tolerance would enable the identification and development of resilient cultivars, resulting in increased canola production. The main objective of the present study was to dissect the genetic basis of seed yield of canola under water-limited conditions. A doubled haploid population derived from a cross between two Australian parental lines, RP04 and Ag-Outback, was evaluated to identify the genetic variation in fractional normalised deviation vegetative index (NDVI), aboveground shoot biomass accumulation, flowering time and plasticity in seed yield under irrigated and rainfed field conditions in two consecutive years. An irrigation treatment was applied at the 50% flowering stage and an incremental drought tolerance index (DTI) was estimated for seed yield. By utilising a genetic linkage map based on 18851 genome-wide DArTseq markers, we identified 25 genomic regions significantly associated with different traits (logarithm of odds (LOD) ≥ 3), accounting for 5.5–22.3% of the genotypic variance. Three significant genomic regions on chromosomes A06, A10 and C04 were associated with DTI for seed yield. Some of the quantitative trait loci (QTL) were localised in the close proximity of candidate genes involved in traits contributing to drought escape and drought avoidance mechanisms, including FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC). Trait-marker associations identified herein can be validated across diverse environments, and the sequence-based markers may be used in a marker assisted selection breeding strategy to enhance drought tolerance in canola breeding germplasm.

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High-throughput phenotyping to dissect genotypic differences in safflower for drought tolerance

PLoS ONE ◽

10.1371/journal.pone.0254908 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0254908

Author(s):

Sameer Joshi ◽

Emily Thoday-Kennedy ◽

Hans D. Daetwyler ◽

Matthew Hayden ◽

German Spangenberg ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

High Throughput ◽

Crop Yields ◽

Geometric Mean ◽

Shoot Biomass ◽

Screening Methods ◽

Tolerance Index ◽

Genotypic Differences ◽

High Throughput Phenotyping

Drought is one of the most severe and unpredictable abiotic stresses, occurring at any growth stage and affecting crop yields worldwide. Therefore, it is essential to develop drought tolerant varieties to ensure sustainable crop production in an ever-changing climate. High-throughput digital phenotyping technologies in tandem with robust screening methods enable precise and faster selection of genotypes for breeding. To investigate the use of digital imaging to reliably phenotype for drought tolerance, a genetically diverse safflower population was screened under different drought stresses at Agriculture Victoria’s high-throughput, automated phenotyping platform, Plant Phenomics Victoria, Horsham. In the first experiment, four treatments, control (90% field capacity; FC), 40% FC at initial branching, 40% FC at flowering and 50% FC at initial branching and flowering, were applied to assess the performance of four safflower genotypes. Based on these results, drought stress using 50% FC at initial branching and flowering stages was chosen to further screen 200 diverse safflower genotypes. Measured plant traits and dry biomass showed high correlations with derived digital traits including estimated shoot biomass, convex hull area, caliper length and minimum area rectangle, indicating the viability of using digital traits as proxy measures for plant growth. Estimated shoot biomass showed close association having moderately high correlation with drought indices yield index, stress tolerance index, geometric mean productivity, and mean productivity. Diverse genotypes were classified into four clusters of drought tolerance based on their performance (seed yield and digitally estimated shoot biomass) under stress. Overall, results show that rapid and precise image-based, high-throughput phenotyping in controlled environments can be used to effectively differentiate response to drought stress in a large numbers of safflower genotypes.

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Maize (Zea mays L.) landraces classified by drought stress tolerance at the seedling stage

Emirates Journal of Food and Agriculture ◽

10.9755/ejfa.2021.v33.i1.2356 ◽

2021 ◽

pp. 29

Author(s):

Víctor A. González Hernández ◽

Eleazar Lugo Cruz ◽

Leopoldo E. Mendoza Onofre ◽

Amalio Santacruz Varela ◽

Ma. Alejandra Gutiérrez Espinosa ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Water Deficit ◽

Recovery Period ◽

Shoot Biomass ◽

Limiting Factor ◽

Stress Recovery ◽

Total Biomass ◽

Maize Landraces ◽

Post Stress

Drought is the main limiting factor for maize production, and climate change can aggravate this water scarcity. One way to mitigate this problem is to plant drought tolerance maize genotypes. In landrace maize grown under rainfed conditions there are drought-adapted genotypes, which can be used in breeding programs for drought tolerance. The objective of this study was to evaluate the effect of an early water deficit on the seedling growth of 41 maize landraces from Nuevo León, Mexico, plus seven varieties, by means of drought tolerance indices based on biomass accumulation during both stress and post-stress recovery period, for identifying tolerant and susceptible genotypes. This study was performed at 2016 in Texcoco, Mexico (19°27’N, 98°54’W, 2241 masl). In the greenhouse, 96 treatments were compared (48 genotypes × two soil water regimes: without and with drought) under randomized complete blocks experimental design. After the drought stress period, normal irrigation was resumed for 15 days for recovery. In maize landraces there is genetic diversity in drought tolerance. Landraces GalTrini and SITexas outstanded as the most water deficit tolerant, whereas landraces Berrones, Rodeo, Sabanilla, Carmen, AraTrini and the inbred line L65 were the most drought susceptible. The total biomass measured before water stress was not related to drought adaptability. This study demonstrates that the post stress recovery is more important in drought stress adaptability than the drought resistance, regarding root biomass, shoot biomass and total biomass. Thus, to include the post stress recovery in drought tolerance studies can produce a more precise genotypic classification for drought stress resistance and adaptability.

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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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Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress

Planta ◽

10.1007/s00425-021-03799-7 ◽

2021 ◽

Vol 255 (1) ◽

Author(s):

Kibrom B. Abreha ◽

Muluken Enyew ◽

Anders S. Carlsson ◽

Ramesh R. Vetukuri ◽

Tileye Feyissa ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Nutritional Quality ◽

Substantial Reduction ◽

Limiting Factor ◽

Molecular Alterations ◽

Germination Process ◽

Effects Of Drought ◽

Grain Yield And Quality ◽

Source Sink

Abstract Main conclusion Droughts negatively affect sorghum’s productivity and nutritional quality. Across its diversity centers, however, there exist resilient genotypes that function differently under drought stress at various levels, including molecular and physiological. Abstract Sorghum is an economically important and a staple food crop for over half a billion people in developing countries, mostly in arid and semi-arid regions where drought stress is a major limiting factor. Although sorghum is generally considered tolerant, drought stress still significantly hampers its productivity and nutritional quality across its major cultivation areas. Hence, understanding both the effects of the stress and plant response is indispensable for improving drought tolerance of the crop. This review aimed at enhancing our understanding and provide more insights on drought tolerance in sorghum as a contribution to the development of climate resilient sorghum cultivars. We summarized findings on the effects of drought on the growth and development of sorghum including osmotic potential that impedes germination process and embryonic structures, photosynthetic rates, and imbalance in source-sink relations that in turn affect seed filling often manifested in the form of substantial reduction in grain yield and quality. Mechanisms of sorghum response to drought-stress involving morphological, physiological, and molecular alterations are presented. We highlighted the current understanding about the genetic basis of drought tolerance in sorghum, which is important for maximizing utilization of its germplasm for development of improved cultivars. Furthermore, we discussed interactions of drought with other abiotic stresses and biotic factors, which may increase the vulnerability of the crop or enhance its tolerance to drought stress. Based on the research reviewed in this article, it appears possible to develop locally adapted cultivars of sorghum that are drought tolerant and nutrient rich using modern plant breeding techniques.

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A Comparative Study for Assessing the Drought-Tolerance of Chickpea Under Varying Natural Growth Environments

Frontiers in Plant Science ◽

10.3389/fpls.2020.607869 ◽

2021 ◽

Vol 11 ◽

Author(s):

Anjuman Arif ◽

Najma Parveen ◽

Muhammad Qandeel Waheed ◽

Rana Muhammad Atif ◽

Irem Waqar ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Seed Yield ◽

Linear Models ◽

Field Conditions ◽

Sufficient Evidence ◽

Breeding Lines ◽

Drought Tolerance Indices ◽

Tolerance Indices ◽

Main Effects

This study was planned with the purpose of evaluating the drought tolerance of advanced breeding lines of chickpea in natural field conditions. Two methods were employed to impose field conditions; the first: simulating drought stress by growing chickpea genotypes at five rainfed areas, with Faisalabad as the non-stressed control environment; and the second: planting chickpea genotypes in spring to simulate a drought stress environment, with winter-sowing serving as the non-stressed environment. Additive main effects and multiplicative interaction (AMMI) and generalized linear models (GLM) models were both found to be equally effective in extracting main effects in the rainfed experiment. Results demonstrated that environment influenced seed yield, number of primary and secondary branches, number of pods, and number of seeds most predominantly; however, genotype was the main source of variation in 100 seed weight and plant height. The GGE biplot showed that Faisalabad, Kallur Kot, and Bhakkar were contributing the most in the GEI, respectively, while Bahawalpur, Bhawana, and Karor were relatively stable environments, respectively. Faisalabad was the most, and Bhakkar the least productive in terms of seed yield. The best genotypes to grow in non-stressed environments were CH39/08, CH40/09, and CH15/11, whereas CH28/07 and CH39/08 were found suitable for both conditions. CH55/09 displayed the best performance in stress conditions only. The AMMI stability and drought-tolerance indices enabled us to select genotypes with differential performance in both conditions. It is therefore concluded that the spring-sown experiment revealed a high-grade drought stress imposition on plants, and that the genotypes selected by both methods shared quite similar rankings, and also that manually computed drought-tolerance indices are also comparable for usage for better genotypic selections. This study could provide sufficient evidence for using the aforementioned as drought-tolerance evaluation methods, especially for countries and research organizations who have limited resources and funding for conducting multilocation trials, and performing sophisticated analyses on expensive software.

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Dissection of Maize Drought Tolerance at the Flowering Stage Using Ge-Nome-Wide Association Study

10.21203/rs.3.rs-1187674/v1 ◽

2021 ◽

Author(s):

Siffat Ullah Khan ◽

Yanxiao Zheng ◽

Zaid Chachar ◽

Xuhuan Zhang ◽

Guyi Zhou ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Candidate Genes ◽

Pyridoxal Phosphate ◽

Association Studies ◽

26S Proteasome ◽

Regulatory Subunit ◽

Tolerance Index ◽

Genome Wide Association Studies ◽

Flowering Stage

Abstract Drought is one of the most critical environmental factors constraining corn production especially when it occurs during flowering, resulting in serious yield losses. In this study, anthesis to silk interval (ASI), plant height (PH), and ear biomass at the silking date (EBM) of 279 inbred lines were evaluated under water-stress (WS) and well-water (WW) field conditions for three consecutive years. Averagely, ASI was extended by 25.96%, ear biomass was decreased by 17.54%, and the PH was reduced by 12.47% under drought stress conditions. Genome wide association studies (GWAS) were carried out using phenotypic values under WS, WW and drought-tolerance index (WS-WW or WS/WW) applying mixed linear model controlling both population structure and relative kinship. Totally, 71, 159, and 21 SNPs were significantly (P < 10-5) associated with ASI, ear biomass, and PH, respectively. Candidate genes encoding ARABIDILLO 1 protein, glycoprotein, Tic22-like and Zinc finger family protein for ASI, and 26S proteasome non-ATPase regulatory subunit-9 for EBM, were identified under both WW and WS conditions. Pyridoxal phosphate transferase was associated with EBM under drought stress treatment in consecutive two years. Furthermore, most candidate genes were evidenced to be drought responsive in the association panel. Meanwhile, the favourable/drought tolerance haplotypes were identified based on haplotype analysis. These findings provide insights into the genetic basis of drought tolerance at the flowering stage especially for the female inflorescence development and will facilitate high drought tolerant maize breeding.

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Association analysis for seed yield, forage yield and traits related to drought tolerance in orchardgrass (Dactylis glomerata)

Crop and Pasture Science ◽

10.1071/cp18178 ◽

2018 ◽

Vol 69 (11) ◽

pp. 1150

Author(s):

Mozhgan Abtahi ◽

Mohammad Mahdi Majidi ◽

Aghafakhr Mirlohi ◽

Fatemeh Saeidnia

Keyword(s):

Water Stress ◽

Drought Tolerance ◽

Association Analysis ◽

Seed Yield ◽

Dactylis Glomerata ◽

Stress Conditions ◽

Forage Yield ◽

Phenotypic Traits ◽

Tolerance Index ◽

Population Structure Analysis

Polycross designs bridge the two usual mapping approaches (bi-parental mapping and association analysis) and increase mapping power by incorporating greater genetic diversity. In this study, we used diverse genotypes selected from polycrossed progenies to identify marker loci associated with a set of seed- and forage-related traits as well as drought tolerance in orchardgrass (Dactylis glomerata L.). Associations were estimated between phenotypic traits and 923 DNA markers (including 446 inter-simple sequence repeats and 477 sequence-related amplified polymorphism markers). Positive relationship was found between forage yield and seed yield under normal and water-stress conditions, indicating that simultaneous improvement of seed and forage yield could be achieved in orchardgrass. The results of population structure analysis identified five main subpopulations possessing significant genetic differences. Under normal and water-stress conditions, respectively, 341 and 359 markers were significantly associated with the studied traits. Most of these markers were associated with more than one trait. Water-environment specificity of trait-associated markers indicates that genotype × environment interactions influence association analysis. However, 75 stable associations were identified across two moisture conditions for traits such as seed and forage yield. Marker–trait association revealed that markers M1/E1-5, M2/E6-5, M3/E4-6, P14-7 and P845-7 were consistently linked with drought-tolerance index. The identified marker alleles associated with multiple traits across environments may be considered for further analysis for their chromosome locations, the corresponding sequences and their potential functions.

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Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes

Genes ◽

10.3390/genes11020182 ◽

2020 ◽

Vol 11 (2) ◽

pp. 182 ◽

Cited By ~ 2

Author(s):

Muthusamy ◽

Yoon ◽

Kim ◽

Jeong ◽

Lee

Keyword(s):

Alternative Splicing ◽

Drought Stress ◽

Stress Response ◽

Drought Tolerance ◽

Brassica Rapa ◽

Target Genes ◽

Tolerance Index ◽

Dependent Manner ◽

Loss Of Function ◽

Splicing Patterns

The emerging evidence has shown that plant serine/arginine-rich (SR) proteins play a crucial role in abiotic stress responses by regulating the alternative splicing (AS) of key genes. Recently, we have shown that drought stress enhances the expression of SR45a (also known as SR-like 3) in Brassica rapa. Herein, we unraveled the hitherto unknown functions of BrSR45a in drought stress response by comparing the phenotypes, chlorophyll a fluorescence and splicing patterns of the drought-responsive genes of Arabidopsis BrSR45a overexpressors (OEs), homozygous mutants (SALK_052345), and controls (Col-0). Overexpression and loss of function did not result in aberrant phenotypes; however, the overexpression of BrSR45a was positively correlated with drought tolerance and the stress recovery rate in an expression-dependent manner. Moreover, OEs showed a higher drought tolerance index during seed germination (38.16%) than the control lines. Additionally, the overexpression of BrSR45a induced the expression of the drought stress-inducible genes RD29A, NCED3, and DREB2A under normal conditions. To further illustrate the molecular linkages between BrSR45a and drought tolerance, we investigated the AS patterns of key drought-tolerance and BrSR45a interacting genes in OEs, mutants, and controls under both normal and drought conditions. The splicing patterns of DCP5, RD29A, GOLS1, AKR, U2AF, and SDR were different between overexpressors and mutants under normal conditions. Furthermore, drought stress altered the splicing patterns of NCED2, SQE, UPF1, U4/U6-U5 tri-snRNP-associated protein, and UPF1 between OEs and mutants, indicating that both overexpression and loss of function differently influenced the splicing patterns of target genes. This study revealed that BrSR45a regulates the drought stress response via the alternative splicing of target genes in a concentration-dependent manner.

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Evaluation of the tolerance of Thai indigenous upland rice germplasm to early drought stress using multiple selection criteria

Plant Genetic Resources ◽

10.1017/s1479262115000428 ◽

2015 ◽

Vol 15 (2) ◽

pp. 109-118 ◽

Cited By ~ 1

Author(s):

Kittichai Narenoot ◽

Tidarat Monkham ◽

Sompong Chankaew ◽

Patcharin Songsri ◽

Wattana Pattanagul ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Selection Criteria ◽

Upland Rice ◽

Block Design ◽

Rice Variety ◽

Tolerance Index ◽

Rice Varieties ◽

Rice Germplasm ◽

Drought Tolerance Index

Drought remains the most important factor that affects rice productivity, especially in rainfed areas, worldwide. Upland rice is one of the crop choices of farmers in the rainfed environment. Although upland rice varieties require less water than lowland rice varieties, yields often remain limited by drought, particularly in the period of early growth. The aims of this study were to identify the traits related to early drought tolerance in upland rice varieties, and to identify the potential sources of germplasm for early drought tolerance. A total of sixty upland rice varieties were planted in a factorial experiment with a randomized complete block design with 3 replications in the rainy seasons of 2011 and 2012, under greenhouse conditions. Based on the drought tolerance index (DTI), the test germplasm sources were classified into three groups: (i) susceptible; (ii) moderately tolerant; (iii) tolerant to drought stress. Grain yield (GY) showed significant negative correlations with the leaf rolling score (r= − 0.623, P< 0.01), the leaf death score (LDS) (r= − 0.673, P< 0.01) and the recovery score (r= − 0.746, P< 0.01), while leaf dry matter (r= 0.698, P< 0.01) and leaf water potential (r= 0.618, P< 0.01) had significant positive correlations with GY. These findings indicate the suitability of the DTI as the selection criteria for early drought tolerance in a breeding programme. In addition, the upland rice germplasm accessions KKU-ULR011, KKU-ULR012, KKU-ULR125, KKU-ULR199 and KKU-ULR292 were identified as having high levels of stability for drought tolerance in both the 2011 and 2012 experiments, suggesting their potential for further use for rice variety improvement for drought tolerance.

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