Key message
Integration of genomic technologies with breeding efforts have been used in recent years for chickpea improvement. Modern breeding along with low cost genotyping platforms have potential ...to further accelerate chickpea improvement efforts.
The implementation of novel breeding technologies is expected to contribute substantial improvements in crop productivity. While conventional breeding methods have led to development of more than 200 improved chickpea varieties in the past, still there is ample scope to increase productivity. It is predicted that integration of modern genomic resources with conventional breeding efforts will help in the delivery of climate-resilient chickpea varieties in comparatively less time. Recent advances in genomics tools and technologies have facilitated the generation of large-scale sequencing and genotyping data sets in chickpea. Combined analysis of high-resolution phenotypic and genetic data is paving the way for identifying genes and biological pathways associated with breeding-related traits. Genomics technologies have been used to develop diagnostic markers for use in marker-assisted backcrossing programmes, which have yielded several molecular breeding products in chickpea. We anticipate that a sequence-based holistic breeding approach, including the integration of functional omics, parental selection, forward breeding and genome-wide selection, will bring a paradigm shift in development of superior chickpea varieties. There is a need to integrate the knowledge generated by modern genomics technologies with molecular breeding efforts to bridge the genome-to-phenome gap. Here, we review recent advances that have led to new possibilities for developing and screening breeding populations, and provide strategies for enhancing the selection efficiency and accelerating the rate of genetic gain in chickpea.
Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide ...association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield.
Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield.
Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Chickpea has a profound nutritional and economic value in vegetarian society. Continuous decline in chickpea productivity is attributed to insufficient genetic variability and different environmental ...stresses. Chickpea like several other legumes is highly susceptible to terminal drought stress. Multiple genes control drought tolerance and ASR gene plays a key role in regulating different plant stresses. The present study describes the molecular characterization and functional role of Abscissic acid and stress ripening (ASR) gene from chickpea (Cicer arietinum) and the gene sequence identified was submitted to NCBI Genbank (MK937569). Molecular analysis using MUSCLE software proved that the ASR nucleotide sequences in different legumes show variations at various positions though ASR genes are conserved in chickpea with only few variations. Sequence similarity of ASR gene to chickpea putative ABA/WDS induced protein mRNA clearly indicated its potential involvement in drought tolerance. Physiological screening and qRT-PCR results demonstrated increased ASR gene expression under drought stress possibly enabled genotypes to perform better under stress. Conserved domain search, protein structure analysis, prediction and validation, network analysis using Phyre2, Swiss-PDB viewer, ProSA and STRING analysis established the role of hypothetical ASR protein NP_001351739.1 in mediating drought responses. NP_001351739.1 might have enhanced the ASR gene activity as a transcription factor regulating drought stress tolerance in chickpea. This study could be useful in identification of new ASR genes that play a major role in drought tolerance and also develop functional markers for chickpea improvement.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches ...for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (
,
,
, and
) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.
Susceptibility to drought stress has restrained chickpea productivity at a global level, and the development of drought-tolerant varieties is essential to maintain its productivity. Therefore, the ...present study was conducted to evaluate genetic divergence in selected genotypes of chickpea and their morpho-physiological responses under irrigated and stressed conditions to identify the traits that account for the better performance of these genotypes under stressed conditions, as well as genotypes with improved drought tolerance. The genotypes were evaluated for two years under irrigated and drought stressed conditions, and significant variation was found amongst the genotypes for different morpho-physiological and yield traits. The maximum reduction was observed for plant yield (33.23%) under stressed conditions. Principle component analysis (PCA)-based biplots and correlation studies established its strong positive correlation with relative water content (RWC), membrane stability index (MSI), chlorophyll index (CI), secondary branches (SB) and yield traits and negative correlations with drought susceptibility index (DSI), days to maturity (DM) and 100 seed weight (100 SW) under drought stress, suggesting their use in selecting drought-tolerant germplasm. Ten genotypes with high values of RWC, MSI, CI, SB, yield traits and lower DSI were identified as drought-tolerant and might serve as ideal donors in the forthcoming breeding of elite chickpea cultivars. The seed-filling stage began earlier in these genotypes, with significantly reduced days to maturity under stressed conditions. Our results indicate selection for earliness offers a promising strategy for the development of drought-tolerant chickpea cultivars.
Botrytis grey mould (BGM), caused by Botrytis cinerea, is emerging as an important disease of chickpea in the northern and eastern parts of the Indian Subcontinent, including Nepal, Bangladesh, ...Pakistan, and in Australia. This fungus has a very broad host range, and sources of complete resistance to the disease have not been found in Cicer arietinum L. germplasm. Resistance to this pathogen has been identified in some wild Cicer species. A set of 371 lines, including 164 landraces and 207 interspecific derivative lines (derived from crosses of cultivated chickpea with C. pinnatifidum, C. judaicum or C. reticulatum) have been screened against Botrytis grey mould under field conditions, and using the cut twig method at the Punjab Agricultural University (PAU), Ludhiana, in 2015-16 and 2016—17. Strong correlations between the two screening methods were indicated by paired-t tests. The Bulked Sample Analysis (BSA) approach was used to screen DNA of the five most resistant and five most susceptible host lines using 300 simple sequence repeat (SSR) markers. Eighty-eight markers were polymorphic. Chi-square statistic values showed strong correlations of TA144, GA102, TA194, TA140 and TR2 with the resistant bulks, signifying their usability as putative markers linked to BGM resistance, and for development of BGM tolerant genotypes in chickpea. Future studies should rapidly ascertain marker trait associations, and identify and develop diagnostic markers that provide an accurate method of molecular tagging BGM resistant genes in chickpea.
Genetic diversity among 40 chickpea (Cicer arietinum L.) genotypes was investigated using 125 microsatellite (SSR, simple sequence repeat) markers. Twenty five polymorphic markers with average ...genetic diversity and PIC (Polymorphic Information Content) value of 0.489 and 0.437, respectively, generated a total of 90 alleles. High PIC and gene diversity (HE) values indicated good variability amongst the chickpea genotypes. Sequential Agglomerative Hierarchical Non-overlapping (SAHN) grouping revealed two main clusters with 29 genotypes in cluster I and 11 genotypes in cluster II. The Cluster analysis did not follow geographical diversity rather it was in agreement for genetic diversity with respect to seed type and parentage/pedigree. Grouping clearly delineated the diverse kabuli and desi genotypes. Molecular variance analysis also indicated 97% variation within the populations and 3% variation among the populations. Principal coordinate analysis (PCoA) divided all the 40 genotypes into three populations based on their seed type and pedigree. The 2D plot largely supported the dendrogram with similar pattern of clustering. It also indicated that the material used was diverse. Thus, the study proved that SSR markers are informative tools for assessing genetic diversity and can be recommended for characterization studies in chickpea.
After drought salinity is the major abiotic stress that severely affects agricultural productivity globally. Chickpea (Cicer arietinum L.) is the important grain legume which suffers approximately ...8-10% of total global yield loss due to salinity. Screening for salt stress is difficult and traits that correlate salinity tolerance are least understood. The present study was carried out at ICAR-IARI, New Delhi 2017-18, deals with the important morphological and physiological traits like RWC (Relative water content), EL (Electrolyte Leakage), Na/K (sodium and potassium ratio) to characterize the salt tolerant genotypes under hydroponic condition which is a quick and easy method to screen large number of chickpea genotypes at initial stage under salt stress condition. Genotypes showing high RWC, low EL and Na/K ratio were tolerant like ICCV 10, JG 11, JG 62 and CSG-8962 whereas genotypes like ICC4958 and Pusa362 fall under moderately tolerant genotypes and DCP 93-3, Pusa 256, Phule G5 and SBD 377 were classified as susceptible genotypes. This study also attempts to understand the candidate genes responsible for salt-stress related pathways in chickpea genotypes based on sequence similarity approach exploiting known salt-stress responsive genes from model crops or other crop species.
Moisture deficit stress is a major abiotic factor affecting muskmelon quality and productivity globally. Here we have examined the response of morpho-physiological traits under moisture deficit ...stress condition in muskmelon parental lines viz., Durgapur Madhu (DM) and BS25 along with F2:3 population derived from their cross for contrasting stress tolerance traits. Moisture stress reduced relative water content significantly (p < 0.01) with variation recorded among population lines. We observed that relative water content showed significant positive correlation (r = 0.34) with proline. A significantly increased value of the proline content (8.68 μg/gm), membrane stability index (27.11 mS/cm) and leaf area (24.43 cm2) were observed in BS25 compared to DM genotype. Some population lines such as L8, L10, L83, L16, L21, L54, and L63 showed significantly higher values for proline content and relative water content in moisture stress condition. We observed variability for different traits in the F2:3 population that allowed selection of individual lines with possibly greater potential of moisture stress tolerance, which can be useful in future breeding programs in muskmelon.
The objective of the study was to validate molecular markers linked to genomic regions controlling flowering time in a set of Recombinant Inbred Lines (RILs) population derived from Pusa 362 (Late) x ...BGD 132 (Early) and 21 diverse genotypes differing in time of flowering in chickpea (Cicer arietinum L.). The study of the polymorphic survey between parents using 27 linked markers of chickpea and Arabidopsis found 8 of them polymorphic. Bulked Segregant Analysis identified TA64 and TA142 as putatively linked to efl3 locus governing early flowering in chickpea that can be utilized for marker assisted selection. The PCR amplification of 6 polymorphic markers in germplasm showed the presence of one or more alleles in many of them (up to 3), indicating the complex nature of flowering time in chickpea. The amplification pattern of CaEfl3a-F1 marker linked to Efl3 early flowering allele of Arabidopsis in 21 chickpea germplasm indicated the presence of some conserved genomic sequences controlling flowering time in the two species.
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