scholarly journals Identification of stable heat tolerance QTLs using inter-specific recombinant inbred line population derived from GPF 2 and ILWC 292

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0254957
Author(s):  
Ashutosh Kushwah ◽  
Dharminder Bhatia ◽  
Inderjit Singh ◽  
Mahendar Thudi ◽  
Gurpreet Singh ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Pollen Viability ◽  
Reproductive Period ◽  
Snp Markers ◽  
Leaf Water Content ◽  
Days To Flowering ◽  
Significant Difference

Heat stress during reproductive stages has been leading to significant yield losses in chickpea (Cicer arietinum L.). With an aim of identifying the genomic regions or QTLs responsible for heat tolerance, 187 F8 recombinant inbred lines (RILs) derived from the cross GPF 2 (heat tolerant) × ILWC 292 (heat sensitive) were evaluated under late-sown irrigated (January-May) and timely-sown irrigated environments (November-April) at Ludhiana and Faridkot in Punjab, India for 13 heat tolerance related traits. The pooled ANOVA for both locations for the traits namely days to germination (DG), days to flowering initiation (DFI), days to 50% flowering (DFF), days to 100% flowering (DHF), plant height (PH), pods per plant (NPP), biomass (BIO), grain yield (YLD), 100-seed weight (HSW), harvest index (HI), membrane permeability index (MPI), relative leaf water content (RLWC) and pollen viability (PV)) showed a highly significant difference in RILs. The phenotyping data coupled with the genetic map comprising of 1365 ddRAD-Seq based SNP markers were used for identifying the QTLs for heat tolerance. Composite interval mapping provided a total of 28 and 23 QTLs, respectively at Ludhiana and Faridkot locations. Of these, 13 consensus QTLs for DG, DFI, DFF, DHF, PH, YLD, and MPI have been identified at both locations. Four QTL clusters containing QTLs for multiple traits were identified on the same genomic region at both locations. Stable QTLs for days to flowering can be one of the major factors for providing heat tolerance as early flowering has an advantage of more seed setting due to a comparatively longer reproductive period. Identified QTLs can be used in genomics-assisted breeding to develop heat stress-tolerant high yielding chickpea cultivars.

scholarly journals Molecular Mapping of QTLs for Heat Tolerance in Chickpea

2018 ◽  
Vol 19 (8) ◽  
pp. 2166 ◽  
Author(s):  
Pronob Paul ◽  
Srinivasan Samineni ◽  
Mahendar Thudi ◽  
Sobhan Sajja ◽  
Abhishek Rathore ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Molecular Mapping ◽  
Recombinant Inbred Lines ◽  
Interval Mapping ◽  
Snp Markers ◽  
Environment Interaction ◽  
Major Qtls ◽  
Heat Tolerant ◽  
Genomic Regions

Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present study was aimed at identifying QTLs associated with heat tolerance in chickpea using 292 F8-9 recombinant inbred lines (RILs) developed from the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant). Phenotyping of RILs was undertaken for two heat-stress (late sown) and one non-stress (normal sown) environments. A genetic map spanning 529.11 cM and comprising 271 genotyping by sequencing (GBS) based single nucleotide polymorphism (SNP) markers was constructed. Composite interval mapping (CIM) analysis revealed two consistent genomic regions harbouring four QTLs each on CaLG05 and CaLG06. Four major QTLs for number of filled pods per plot (FPod), total number of seeds per plot (TS), grain yield per plot (GY) and % pod setting (%PodSet), located in the CaLG05 genomic region, were found to have cumulative phenotypic variation of above 50%. Nineteen pairs of epistatic QTLs showed significant epistatic effect, and non-significant QTL × environment interaction effect, except for harvest index (HI) and biomass (BM). A total of 25 putative candidate genes for heat-stress were identified in the two major genomic regions. This is the first report on QTLs for heat-stress response in chickpea. The markers linked to the above mentioned four major QTLs can facilitate marker-assisted breeding for heat tolerance in chickpea.

scholarly journals Genotyping by sequencing of 393 Sorghum bicolor BTx623 × IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection

2018 ◽  
Author(s):  
WenQian Kong ◽  
Changsoo Kim ◽  
Dong Zhang ◽  
Hui Guo ◽  
Xu Tan ◽  
...  
Keyword(s):  
Flowering Time ◽  
Plant Height ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Ril Population ◽  
Trait Locus ◽  
Number Of Individuals ◽  
Syntenic Regions

AbstractWe describe a genetic map with a total of 381 bins of 616 genotyping by sequencing (GBS)-based SNP markers in a F6-F8 recombinant inbred line (RIL) population of 393 individuals derived from crossing S. bicolor BTx623 to S. bicolor IS3620C, a guinea line substantially diverged from BTx623. Five segregation distorted regions were found with four showing enrichment for S. bicolor alleles, suggesting possible selection during formation of this RIL population. A quantitative trait locus (QTL) study with this number of individuals, tripled relative to prior studies of this cross, provided resources, validated previous findings, and demonstrated improved power to detect plant height and flowering time related QTLs relative to other published studies. An unexpected low correlation between flowering time and plant height permitted us to separate QTLs for each trait and provide evidence against pleiotropy. Ten non-random syntenic regions conferring QTLs for the same trait suggest that those QTLs may represent alleles at genes functioning in the same manner since the 96 million year ago genome duplication that created these syntenic relationships, while syntenic regions conferring QTLs for different trait may suggest sub-functionalization after duplication. Collectively, this study provides resources for marker-assisted breeding, as well as a framework for fine mapping and subsequent cloning of major genes for important traits such as plant height and flowering time in sorghum.

QTL mapping of early flowering and resistance to ascochyta blight in chickpea

Genome ◽  
2016 ◽  
Vol 59 (6) ◽  
pp. 413-425 ◽  
Author(s):  
Ketema Daba ◽  
Amit Deokar ◽  
Sabine Banniza ◽  
Thomas D. Warkentin ◽  
Bunyamin Tar’an
Keyword(s):  
Phenotypic Variation ◽  
Recombinant Inbred Lines ◽  
Ascochyta Blight ◽  
Snp Markers ◽  
Chromosome 8 ◽  
Flowering Plant ◽  
Blight Resistance ◽  
Days To Flowering ◽  
Growing Seasons ◽  
Wide Range

In western Canada, chickpea (Cicer arietinum L.) production is challenged by short growing seasons and infestations with ascochyta blight. Research was conducted to determine the genetic basis of the association between flowering time and reaction to ascochyta blight in chickpea. Ninety-two chickpea recombinant inbred lines (RILs) developed from a cross between ICCV 96029 and CDC Frontier were evaluated for flowering responses and ascochyta blight reactions in growth chambers and fields at multiple locations and during several years. A wide range of variation was exhibited by the RILs for days to flower, days to maturity, node of first flowering, plant height, and ascochyta blight resistance. Moderate to high broad sense heritability was estimated for ascochyta blight reaction (H2 = 0.14–0.34) and for days to flowering (H2 = 0.45–0.87) depending on the environments. Negative correlations were observed among the RILs for days to flowering and ascochyta blight resistance, ranging from r = −0.21 (P < 0.05) to −0.58 (P < 0.0001). A genetic linkage map consisting of eight linkage groups was developed using 349 SNP markers. Seven QTLs for days to flowering were identified that individually explained 9%–44% of the phenotypic variation. Eight QTLs were identified for ascochyta blight resistance that explained phenotypic variation ranging from 10% to 19%. Clusters of QTLs for days to flowering and ascochyta blight resistances were found on chromosome 3 at the interval of 8.6–23.11 cM and on chromosome 8 at the interval of 53.88–62.33 cM.

scholarly journals Identification of QTL Underlying Seed Micronutrients Accumulation in ‘MD 96-5722’ by ‘Spencer’ Recombinant Inbred Lines of Soybean

2017 ◽  
Vol 1 (3) ◽  
pp. 39-49 ◽  
Author(s):  
Nacer Bellaloui ◽  
Laila Khandaker ◽  
Masum Akond ◽  
Stella K. Kantartzi ◽  
Khalid Meksem ◽  
...  
Keyword(s):  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Snp Markers ◽  
Linkage Groups ◽  
Seed Industry ◽  
Similar Region ◽  
Nutritional Qualities ◽  
Genetic Mechanisms ◽  
Nutritional Needs

Genetic mapping of quantitative trait loci (QTL) associated with seed nutrition levels is almost non-existent. The objective of this study was to identify QTLs associated with seed micronutrients (iron, Fe; zinc, Zn; bororn, B; manganese, Mn; and copper, Cu) accumulation (concentration) in a population of 92 F5:7 recombinant inbred lines (RILs) that derived from a cross between MD 96-5722 (MD) and ‘Spencer’. For this purpose, a genetic linkage map based on 5,376 Single Nucleotide Polymorphism (SNP) markers was constructed using the Illumina Infinium SoySNP6K BeadChip array. The RILs were genotyped using 537 polymorphic, reliably segregating SNP markers. A total of 23 QTLs for micronutrients Fe, Zn, B, Mn, and Cu have been identified and mapped on eight linkage groups (LGs) of the soybean genome. Five QTLs were detected for Fe (qIRO001- qIRO005) on LGs N, A1, K, J, and G. Seven QTLs for Zn (qZIN001-qZIN007) on LGs D1a (Chr 1), N (Chr 3), F (Chr 5), B2 (Chr 14), J (Chr 16), A1 (Chr 5), and K (Chr 9). Two QTLs for B (qBOR001 and qBOR002) were detected on LGs N and A1. Four QTLs were detected for Mn (qMAN001-qMAN004) on LGs N, A1, K, and J, and five QTLs were detected for Cu (qCOP001- qCOP005) on LGs N, A1, K, J, and G). It was observed that the four QTLs for Zn, Cu, Fe, and Mn on LGs N (Chr 3), LG A1 (Chr 5), and LG J (Chr 16) were clustered in a similar region of the linkage groups, suggesting possible shared physiological and genetic mechanisms. The QTLs detected in this study are novel and will contribute to our understanding of the genetic basis of seed mineral nutrition. This research would allow breeders to efficiently select for higher seed nutritional qualities to meet the seed industry and human and livestock nutritional needs.

Heat-stress-induced reproductive failures in chickpea (Cicer arietinum) are associated with impaired sucrose metabolism in leaves and anthers

2013 ◽  
Vol 40 (12) ◽  
pp. 1334 ◽  
Author(s):  
Neeru Kaushal ◽  
Rashmi Awasthi ◽  
Kriti Gupta ◽  
Pooran Gaur ◽  
Kadambot H. M. Siddique ◽  
...  
Keyword(s):  
Heat Stress ◽  
Cicer Arietinum ◽  
Pollen Viability ◽  
Photochemical Efficiency ◽  
Membrane Integrity ◽  
Reproductive Stage ◽  
Leaf Water Content ◽  
Sucrose Content ◽  
Stress Injury

Chickpea (Cicer arietinum L.), in its reproductive stage, is sensitive to heat stress (32/20°C or higher as day/night temperatures) with consequent substantial loss of potential yields at high temperatures. The physiological mechanisms associated with reproductive failures have not been established: they constitute the basis of this study. Here, we initially screened a large core-collection of chickpea against heat stress and identified two heat-tolerant (ICC15614, ICCV. 92944) and two heat-sensitive (ICC10685, ICC5912) genotypes. These four genotypes were sown during the normal time of sowing (November–March) and also late (February–April) to expose them to heat stress during reproductive stage (>32/20°C). The genotypes were assessed for damage by heat stress to the leaves and reproductive organs using various indicators of stress injury and reproductive function. In the heat-stressed plants, phenology accelerated as days to flowering and podding, and biomass decreased significantly. The significant reduction in pod set (%) was associated with reduced pollen viability, pollen load, pollen germination (in vivo and in vitro) and stigma receptivity in all four genotypes. Heat stress inhibited pollen function more in the sensitive genotypes than in the tolerant ones, and consequently showed significantly less pod set. Heat stress significantly reduced stomatal conductance, leaf water content, chlorophyll, membrane integrity and photochemical efficiency with a larger effect on heat-sensitive genotypes. Rubisco (carbon-fixing enzyme) along with sucrose phosphate synthase (SPS) and sucrose synthase (SS) (sucrose-synthesising enzymes) decreased significantly in leaves due to heat stress leading to reduced sucrose content. Invertase, a sucrose-cleaving enzyme, was also inhibited along with SPS and SS. The inhibition of these enzymes was significantly greater in the heat-sensitive genotypes. Concurrently, the anthers of these genotypes had significantly less SPS and SS activity and thus, sucrose content. As a result, pollen had considerably lower sucrose levels, resulting in reduced pollen function, impaired fertilisation and poor pod set in heat-sensitive genotypes.

scholarly journals Accelerating Breeding for Heat Tolerance in Tomato (Solanum lycopersicum L.): An Integrated Approach

Agronomy ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 720 ◽  
Author(s):  
Mathieu Anatole Tele Ayenan ◽  
Agyemang Danquah ◽  
Peter Hanson ◽  
Charles Ampomah-Dwamena ◽  
Fréjus Ariel Kpêdétin Sodedji ◽  
...  
Keyword(s):  
Heat Stress ◽  
Confidence Interval ◽  
Heat Tolerance ◽  
Pollen Viability ◽  
Total Yield ◽  
Integrated Approach ◽  
Crop Productivity ◽  
Limiting Factor ◽  
Substitution Lines ◽  
Advanced Backcross

Heat stress is a major limiting factor for crop productivity. Tomato is highly sensitive to heat stress, which can result in a total yield loss. To adapt to current and future heat stress, there is a dire need to develop heat tolerant cultivars. Here, we review recent attempts to improve screening for heat tolerance and to exploit genetic and genomic resources in tomatoes. We provide key factors related to phenotyping environments and traits (morphological, physiological, and metabolic) to be considered to identify and breed thermo-tolerant genotypes. There is significant variability in tomato germplasm that can be harnessed to breed for thermo-tolerance. Based on our review, we propose that the use of advanced backcross populations and chromosome segments substitution lines is the best means to exploit variability for heat tolerance in non-cultivated tomato species. We applied a meta quantitative trait loci (MQTL) analysis on data from four mapping experiments to co-localize QTL associated with heat tolerance traits (e.g., pollen viability, number of pollen, number of flowers, style protrusion, style length). The analysis revealed 13 MQTL of which 11 were composed of a cluster of QTL. Overall, there was a reduction of about 1.5-fold in the confidence interval (CI) of the MQTL (31.82 cM) compared to the average CI of individual QTL (47.4 cM). This confidence interval is still large and additional mapping resolution approaches such as association mapping and multi-parent linkage mapping are needed. Further investigations are required to decipher the genetic architecture of heat tolerance surrogate traits in tomatoes. Genomic selection and new breeding techniques including genome editing and speed breeding hold promise to fast-track development of improved heat tolerance and other farmer- and consumer-preferred traits in tomatoes.

Phenotyping from lab to field – tomato lines screened for heat stress using Fv/Fm maintain high fruit yield during thermal stress in the field

2019 ◽  
Vol 46 (1) ◽  
pp. 44 ◽  
Author(s):  
Damodar Poudyal ◽  
Eva Rosenqvist ◽  
Carl-Otto Ottosen
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Pollen Viability ◽  
Crop Improvement ◽  
Field Performance ◽  
Net Photosynthesis ◽  
Plant Size ◽  
Fruit Yield ◽  
Heat Sensitivity ◽  
Solanum Lycopersicum L

This study aimed to phenotype young tomato (Solanum lycopersicum L.) plants for heat tolerance by measuring Fv/Fm after short-term heat treatments in climate chambers and selected sensitive (low Fv/Fm) and tolerant (high Fv/Fm) cultivars to investigate their in-field performance. Twenty-eight genotypes were phenotyped at 40:28°C for 2 days in climate chambers. A second screening (four high Fv/Fm and four low Fv/Fm genotypes) was conducted for 4 days at 38:28°C, followed by 5 days’ recovery (26:20°C). The tolerant genotypes maintained high net photosynthesis (PN) and increased stomatal conductance (gs) at 38°C, allowing better leaf cooling. Sensitive genotypes had lower Fv/Fm and PN at 38°C, and gs increased less than in the tolerant group, reducing leaf cooling. Under controlled conditions, all eight genotypes had the same plant size and pollen viability, but after heat stress, plant size and pollen viability reduced dramatically in the sensitive group. Two tolerant and two sensitive genotypes were grown in the field during a heat wave (38:26°C). Tolerant genotypes accumulated more biomass, had a lower heat injury index and higher fruit yield. To our knowledge, this is the first time screening for heat tolerance by Fv/Fm in climate chambers was verified by a field trial under natural heat stress. The differences after heat stress in controlled environments were comparable to those in yield between tolerant and sensitive groups under heat stress in the field. The results suggest that Fv/Fm is effective for early detection of heat tolerance, and screening seedlings for heat sensitivity can speed crop improvement.

scholarly journals Genetic Mapping of QTL Associated with Seed Macronutrients Accumulation in ‘MD 96-5722’ by ‘Spencer’ Recombinant Inbred Lines of Soybean

2017 ◽  
Vol 3 (2) ◽  
pp. 224-235 ◽  
Author(s):  
Nacer Bellaloui ◽  
Laila Khandaker ◽  
Masum Akond ◽  
Stella K. Kantartzi ◽  
Khalid Meksem ◽  
...  
Keyword(s):  
Recombinant Inbred ◽  
Genetic Relationships ◽  
Recombinant Inbred Lines ◽  
Soybean Seed ◽  
Peak Position ◽  
Inbred Lines ◽  
Snp Markers ◽  
Nutrition Quality ◽  
C And N ◽  
N:S Ratio

Research of quantitative trait loci (QTL) for macronutrient accumulation in soybean seed is limited. Therefore, the objective of this research was to identify QTL related to macronutrients (N, C, S, P, K, Ca, and Mg) in seeds in 92 F5:7 recombinant inbred lines (RILs) developed from a cross between MD 96-5722 (MD) and Spencer using a total 5,376 Single Nucleotide Polymorphism (SNP) markers. A genetic linkage map based on SNP markers was constructed using the Illumina Infinium SoySNP6K BeadChip Array. The RILs were genotyped using 537 polymorphic, reliably segregating SNP markers. A total of 8 QTL for K (qPOT001-qPOT008) were identified on LGs D1b (Chr 1), N (Chr 3), A1 (Chr 5), O (Chr 10), F (Chr 13), B2 (Chr 14), and J (Chr 16). Four QTL for Mg (qMAG001-qMAG004) were identified on LGs N (Chr 3), A1 (Chr 5), J (Chr 16), and G (Chr 18). One QTL for P (qPHO001), one for C on LG J (Chr 16), one for N (qNIT001) and S (qSUL001) on the same LG J (Chr 16), and one QTL for Ca (qCAL001) on LG G (Chr 18). K and Mg QTL were clustered together on LG A1 (Chr 5) with a peak position of 9.50 cM and  LOD support interval of 8.50-9.50 cM. Similar observation was noticed for P, K, Mg, C, N, and S, where the QTL were clustered on LG J (Chr 16) with peak position of 11 cM for K, P, and S, and 10 cM for C and N, and 12 cM for Mg. The LOD support intervals for all these clustered QTL were between 8.90 and 12.30 cM. The QTL clustering of these nutrients suggests possible common physiological and genetic relationships, suggesting possible similar metabolic processes and pathways  for these nutrients. The inverse relationships between N:S ratio and all nutrients suggest possible use of N:S ratio as a measure for higher nutrients accumulation in seed. Since most of QTL identified in this study were not previously reported, this research will further help breeders to improve nutrient accumulation in seeds and contribute to our understanding of the physiological and genetic bases of seed nutrition quality.

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