QTL Analysis Molecular Genetics Diversity and Agro-physiological Characterizations of Heat Tolerance in Chickpea (Cicer Arietinum L.)
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Date
2021-12-08
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Addis Ababa University
Abstract
Chickpea is a cheap source of protein and rich in minerals for people living in developing countries. A major agronomic challenge for chickpea production is temperatures above 35°C, which reduced growth, fertility, development, production and productivity of cultivated chickpea. Besides, domesticated chickpea changes in the nature and intensity of selection during domestication and breeding that constrain the ability to expand the cultivation of crops into arid and semi-arid environments. Therefore, the objectives of the present study were to introgress wild genes into the cultivated gene pool via genomics assisted breeding, assess the molecular genetic diversity and determine the population structures of large collections of chickpea germpalsms; screen heat tolerant genotypes and assess phenotypic variations from all sources of chickpea germplam accessions under heat stress environments; and understand the mechanisms of heat tolerance.
A total of 480 chickpea accessions that comprised of 440 F3 lines of C. arietinum x C. reticulatum (17 AR families) and 33 F3 lines of C. arietinum x C. echinospermum (3 AE families), and seven standard heat tolerant and sensitive checks which were grown in two replications at ICRISAT, Hyderabad, India under heat stress conditions. GBS SNPs of 1445 and
1541 were used in AR and AE families, respectively for linkage map construction and QTL mapping. Among the 20 families, 9xKalkan_064 was consistently found to be the most heat tolerant pre-breeding family, while 9xKarabache_081A and 9xDerei_072 were in the ranges of heat sensitive to moderately heat tolerant families. A total of 194 QTLs were detected for 16 traits out of which 38 QTLs had pleotropic effects. The associated SNP markers with pleotropic loci are important for simultaneous selection of genotypes having more than two related traits for heat stress breeding in chickpea.
In order to assess the existing molecular genetic diversity and to determine population structure in selected Ethiopian chickpea germplasm accessions (118), a set of 46 simple sequence repeat (SSR) markers equally distributed on chickpea genome were genotyped. A total of 572 alleles were detected from 46 SSR markers and the number of alleles per locus varied from 2 (ICCM0289) to 28 (TA22). The average numbers of alleles per locus, polymorphism information content and expected heterozygosity were 12, 0.684 and 0.699, respectively. Phylogenetic analysis grouped the 118 chickpea genotypes from diverse sources into three evolutionary and/or biological groups (improved desi, improved kabuli and landraces). Population structure analysis revealed six sub-populations from 118 chickpea genotypes used in this study. AMOVA revealed that 57%, 29% and 14% of the total genetic variations were observed among individuals, within populations and among populations.
A total of 121 chickpea genotypes were assessed at three field sites in Ethiopia, under heat stressed and non-stressed conditions and 57 genotypes were assessed under high heat stressed conditions at ICRISAT, Hyderabad, India. The results showed that the chickpea genotypes were
severely impacted by excessive heat at Hyderabad as compared to those planted under non-heat stressed conditions in Debre Zeit, Ethiopia. At extremely high temperatures, chickpea plants exhibited reduced floral initiation, arrested seed and pod development, shortened life cycles, and reduced plant height, seed size, grain yield and yield related traits. Across stressed and non-stressed environments, there were highly significant differences among the genotypes for most of the traits (ANOVA, P≤0.001). Under heat stressed environments, DZ-Cr-0034 was found to be a highly tolerant, while DZ-Cr-0026 was found to be a highly sensitive genotype. Genetic diversity among the genotypes were determined using 5,722 SNPs, revealing a single group of Ethiopian genotypes with small number of cultivars showing introgression from Middle Eastern germplasm.
At the reproductive developmental stages, a total of 13 physiological parameters were measured for 47 chickpea accessions that were grown from February to May, 2019 under a heat stressed environment, Werer (Ethiopia), using a high throughput phenotyping tool (MultispeQ). Based on the physiological responses of chickpea accessions under heat stressed environment, it was confirmed that DZ-2012-ck-0034 and JG 14 were found to be the most heat tolerant, while DZ-2012-ck-0026 and ICC 4567 were the most heat sensitive genotypes. Unlike heat sensitive genotypes, heat tolerant genotypes exhibited high mean values for effective quantum yield of photosystem II (Phi2), chlorophyll fluorescence decline ratio (RFd), coefficients for photochemical quenching (qP and qL), chlorophyll fluorescence (Fv/Fm), pod set and low mean values for regulated (PhiNPQ) and non-regulated heat dissipations (PhiNO).
Reproductive traits were studied under heat stressed conditions with 17 and 47 chickpea accessions that were grown at ICRISAT (Hyderbad, India) and Werer (Ethiopia), respectively. The pollen viability study was carried out by using 2% acetocarmine stain. The quantity of pollens per flower was counted with haemocytometer. In vitro pollen germination was determined by using a modified Brewbaker and Kwack liquid medium. Under heat stressed condition, at ICRISAT (Hyderabad, India), the F3 individuals of 9xCudiB_022C family had the highest average percentage of pollen viability (94%) which was associated with high pod set (80%). However, 9xKarabche_081A (9%) and ICC 4567 (10%) had low average percentage of pollen viability which was also associated with low pod set (0-10%). The mean values of the pollen cells per flower, in vitro pollen germination and pod set of the segregating progenies were higher than the landraces, lines and varieties which implied that the segregating wild progenies resisted the heat stress i.e. linked traits can be introgressed into cultivars in order to enhance thermotolerance.
The present study revealed that the Ethiopian germplasm accessions have genetic variability for heat tolerance that can be harnessed to meet expected shifts towards warmer climate. The physiological and reproductive traits might enhance the efficiency and accuracy of breeding in chickpea for screening and identifying of tolerant genotypes and help to understand the mechanisms of heat tolerance under heat stress conditions and contribuite to climate resilient agriculture.
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Keywords
GBS Snps, Mechanisms of Heat Tolerance, Molecular Genetic Diversity, Population Structure, QTL Analysis, RAD-Seq