Delineating Marker-Trait Associations for Fusarium Wilt in Chickpea Using the Axiom® CicerSNP Array.

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. ciceri is a devastating disease of chickpea (Cicer arietinum). To identify promising resistant genotypes and genomic loci for FW resistance, a core set of 179 genotypes of chickpea was tested for FW reactions at the seedling and reproductive stages under field conditions and controlled conditions in the greenhouse. Our results revealed that at the seedling stage, most of the genotypes were resistant, whereas at the reproductive stage, most of the genotypes were susceptible. Genotyping using a 50K Axiom® CicerSNP Array and trait data of FW together led to the identification of 26 significant (P ≤ E-05) marker-trait associations (MTAs) for FW resistance. Among the 26 MTAs, 12 were identified using trait data recorded in the field (three at the seedling and nine at the reproductive stage), and 14 were identified using trait data recorded under controlled conditions in the greenhouse (six at the seedling and eight at the reproductive stage). The phenotypic variation explained by these MTAs varied from 11.75 to 15.86%, with an average of 13.77%. Five MTAs were classified as major, explaining more than 15% of the phenotypic variation for FW, and two were declared stable, being identified in two environments. One of the promising stable and major MTAs (Affx_123280060) detected in field conditions at the reproductive stage was also detected in greenhouse conditions at the seedling and reproductive stages. The stable and major (>15% PVE) MTAs can be used in chickpea breeding programs.

Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.).

Chickpea is the most important nutrient-rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with a Axiom(®)50K CicerSNP array and trait phenotyped in two different environments for four seed micronutrients (Zn, Cu, Fe and Mn). The trait data and high-throughput 50K SNP genotypic data were used for the genome-wide association study (GWAS). The study led to the discovery of genes/QTLs for seed Zn, Cu, Fe and Mn, concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all four micronutrient concentrations (P ≤ 0.05). The mean concentrations of seed Zn, Cu, Fe and Mn pooled over the 2 years were 45.9 ppm, 63.8 ppm 146.1 ppm, and 27.0 ppm, respectively. The analysis of results led to the identification of 35 SNPs significantly associated with seed Zn, Cu, Fe and Mn concentrations. Among these 35 marker-trait associations (MTAs), 5 were stable (consistently identified in different environments), 6 were major (explaining more than 15% of the phenotypic variation for an individual trait) and 3 were both major and stable MTAs. A set of 6 MTAs, MTAs (3 for Mn, 2 for Fe, and 1 for Cu) reported by us during the present study have been also reported in the same/almost same genomic regions in earlier studies and therefore declared as validated MTAs. The stable, major and validated MTAs identified during the present study will prove useful in future chickpea molecular breeding programs aimed at enhancing the seed nutrient density of chickpea.

SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas.

BACKGROUND: The exploration of genetic diversity is the key source of germplasm conservation and potential to broaden its genetic base. The globally growing demand for chickpea suggests superior/climate-resilient varieties, which in turn necessitates the germplasm characterization to unravel underlying genetic variation. METHODOLOGY AND RESULTS: A chickpea core collection comprising of diverse 192 accessions which include cultivated Cicer arietinum, and wild C. reticulatum, C. echinospermum, and C. microphyllum species were investigated to analyze their genetic diversity and relationship, by assaying 33 unlinked simple sequence repeat (SSR) markers. The results amplified a total of 323 alleles (Na), ranging from 2 to 8 with an average of 4.25 alleles per locus. Expected heterozygosity (He) differed from 0.46 to 0.86 with an average of 0.68. Polymorphic information content (PIC) ranged from 0.73 to 0.98 with an average of 0.89. Analysis of molecular variance (AMOVA) showed that most of the variation was among individuals (87%). Cluster analysis resulted in the formation of four distinct clusters. Cluster I represented all cultivated and clusters II, III, and IV comprised a heterogeneous group of cultivated and wild chickpea accessions. CONCLUSION: We report considerable diversity and greater resolving power of SSR markers for assessing variability and interrelationship among the chickpea accessions. The chickpea core is expected to be an efficient resource for breeders for broadening the chickpea genetic base and could be useful for selective breeding of desirable traits and in the identification of target genes for genomics-assisted breeding.

Vitamin D status among Kashmiri tribal population: A cross-sectional community-based study.

Background & objectives: Vitamin D deficiency (VDD) is prevalent across all age groups in general population of India but studies among tribal populations are scanty. This study aimed to evaluate the prevalence of VDD in the indigenous tribal population of the Kashmir valley and examine associated risk factors. Methods: In this cross-sectional investigation, a total of 1732 apparently healthy tribal participants (n=786 males and n=946 females) were sampled from five districts of Kashmir valley by using probability proportional to size method. Serum 25-hydroxy vitamin D (25(OH)D) levels were classified as per the Endocrine Society (ES) recommendations: deficiency (<20 ng/ml), insufficiency (20-30 ng/ml) and sufficiency (>30 ng/ml). The serum 25(OH)D levels were assessed in relation to various demographic characteristics such as age, sex, education, smoking, sun exposure, body mass index and physical activity. Results: The mean age of the male participants was 43.79±18.47 yr with a mean body mass index (BMI) of 20.50±7.53 kg/m[2], while the mean age of female participants was 35.47±14.92 yr with mean BMI of 22.24±4.73 kg/m2. As per the ES guidelines 1143 of 1732 (66%) subjects had VDD, 254 (14.71%) had insufficient and 334 (19.3%) had sufficient serum 25(OH)D levels. VDD was equally prevalent in male and female participants. Serum 25(OH)D levels correlated positively with serum calcium, phosphorous and negatively with serum alkaline phosphatase. Gender, sun exposure, altitude, physical activity and BMI did not seem to contribute significantly to VDD risk. Interpretation & conclusions: VD deficiency is highly prevalent among Kashmiri tribals, although the magnitude seems to be lower as compared to the general population. These preliminary data are likely to pave way for further studies analyzing the impact of vitamin D supplementation with analysis of functional outcomes.

Assessment of cold tolerance in chickpea (Cicer spp.) grown under cold/freezing weather conditions of North-Western Himalayas of Jammu and Kashmir, India.

Chickpea is one of the most important grain legume crops in the world. India is the largest producer, consumer as well as importer of chickpea. Cold stress (temperature < 15 °C) is one of the important abiotic stresses limiting chickpea production by hampering its growth and vigor at all phenological stages. This study was aimed to characterize a diverse set of 366 chickpea genotypes for cold tolerance and identify most promising cold tolerant chickpea genotypes in the Western-Himalayas of Jammu and Kashmir, India. The 366 genotypes used during the present study including genotypes belonging to cultivated, primary and secondary gene pools of chickpea. Two important approaches were used including visual screening under field conditions and screening under controlled conditions by measuring cell membrane stability through electrolyte leakage tests. The analysis of trait data collected through both the approaches led to the identification of five most promising/candidate cold tolerant chickpea genotypes including one wild genotype "Ortan-066" from secondary gene pool species (C. echinospermum), one wild genotype "Cudi 1-022" from primary gene pool species (C. reticulatum) and three genotypes (IC 116783, ICC 15200 and AGBLG 170004) from the cultivated species (Cicer arietinum). Wild genotype "Ortan-066" was found best cold tolerance source with the mean Cold Tolerance Rating (CTR) of 2 and Electrolyte Leakage Index (ELI) of 10.82%, followed by wild genotype "Cudi 1-022" (CTR = 3, ELI = 18.89%), and three cultivated genotypes viz., IC 116783, ICC 15200 and AGBL-G-170004, with the mean CTR of 3 and an estimated mean ELI of 21.26%, 21.58% and 21.94%, respectively. The promising, candidate cold tolerant genotypes identified during the present study could be used in chickpea breeding programs aimed at improving cold tolerance of cultivated chickpea worldwide. The candidate lines can be also used for developing bi-parental mapping populations, wild × cultivated introgression lines, transcriptomics and for differential expression analysis of cold tolerant genes in chickpea. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-00997-1.

Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas.

The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer's selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity, He) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker-trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield.

High-throughput phenotyping for crop improvement in the genomics era.

Tremendous progress has been made with continually expanding genomics technologies to unravel and understand crop genomes. However, the impact of genomics data on crop improvement is still far from satisfactory, in large part due to a lack of effective phenotypic data; our capacity to collect useful high quality phenotypic data lags behind the current capacity to generate high-throughput genomics data. Thus, the research bottleneck in plant sciences is shifting from genotyping to phenotyping. This article review the current status of efforts made in the last decade to systematically collect phenotypic data to alleviate this 'phenomics bottlenecks' by recording trait data through sophisticated non-invasive imaging, spectroscopy, image analysis, robotics, high-performance computing facilities and phenomics databases. These modern phenomics platforms and tools aim to record data on traits like plant development, architecture, plant photosynthesis, growth or biomass productivity, on hundreds to thousands of plants in a single day, as a phenomics revolution. It is believed that this revolution will provide plant scientists with the knowledge and tools necessary for unlocking information coded in plant genomes. Efforts have been also made to present the advances made in the last 10 years in phenomics platforms and their use in generating phenotypic data on different traits in several major crops including rice, wheat, barley, and maize. The article also highlights the need for phenomics databases and phenotypic data sharing for crop improvement. The phenomics data generated has been used to identify genes/QTL through QTL mapping, association mapping and genome-wide association studies (GWAS) for genomics-assisted breeding (GAB) for crop improvement.

Pattern of glomerulonephritis in the Kashmir valley.

Glomerulonephritis (GN) is a common cause of end-stage kidney disease (ESKD) that can affect patients at any age. With respect to ESKD, there are significant global variations in the percentage of the incident and prevalent patients secondary to GN. The present study was therefore conducted to know the pattern of GN in the Kashmir valley. Retrospective study was conducted in the tertiary center Sher-I-Kashmir Institute of Medical Sciences of Kashmir valley which included cases of different types of GN diagnosed on histopathology over a period of three years. Basic demographic profile including age, sex, clinical presentation, relevant investigations, and the histopathological type of GN was noted for each patient. Histopathological examination due to various nonneoplastic renal diseases was done in 336 cases and out of these, glomerular diseases were diagnosed in 298 cases. Proteinuria and edema was the most common presentation. Primary GN was observed in 81% of cases and secondary GN in 16% of cases. IgA nephropathy was the most common primary GN 42% and nephropathy due to lupus was the most common secondary GN. The study concluded that primary GN is the most common primary renal disease with IgA as the most common primary GN and most presented as renal failure, highest until date recorded in India and lupus nephritis as the most common secondary GN which is similar to other studies from India and other regions of the world. This study may be useful to pathologists, nephrologists, and health care providers to formulate a basic platform for effective diagnostic, therapeutic, and research base for glomerular diseases so as to prevent its complications.

Gene/QTL discovery for Anthracnose in common bean (Phaseolus vulgaris L.) from North-western Himalayas.

Common bean (Phaseolus vulgaris L.) is one of the most important grain legume crops in the world. The beans grown in north-western Himalayas possess huge diversity for seed color, shape and size but are mostly susceptible to Anthracnose disease caused by seed born fungus Colletotrichum lindemuthianum. Dozens of QTLs/genes have been already identified for this disease in common bean world-wide. However, this is the first report of gene/QTL discovery for Anthracnose using bean germplasm from north-western Himalayas of state Jammu & Kashmir, India. A core set of 96 bean lines comprising 54 indigenous local landraces from 11 hot-spots and 42 exotic lines from 10 different countries were phenotyped at two locations (SKUAST-Jammu and Bhaderwah, Jammu) for Anthracnose resistance. The core set was also genotyped with genome-wide (91) random and trait linked SSR markers. The study of marker-trait associations (MTAs) led to the identification of 10 QTLs/genes for Anthracnose resistance. Among the 10 QTLs/genes identified, two MTAs are stable (BM45 & BM211), two MTAs (PVctt1 & BM211) are major explaining more than 20% phenotypic variation for Anthracnose and one MTA (BM211) is both stable and major. Six (06) genomic regions are reported for the first time, while as four (04) genomic regions validated the already known QTL/gene regions/clusters for Anthracnose. The major, stable and validated markers reported during the present study associated with Anthracnose resistance will prove useful in common bean molecular breeding programs aimed at enhancing Anthracnose resistance of local bean landraces grown in north-western Himalayas of state Jammu and Kashmir.

Pattern of urinary albumin excretion in normotensive young and adolescent Indian women with polycystic ovary syndrome.

OBJECTIVE: Polycystic ovarian syndrome (PCOS) is a clinically heterogeneous endocrine disorder affecting up to 4-8% of women of reproductive age. The aim of this study was to evaluate the presence of microalbuminuria in women with PCOS and study its correlation with the various metabolic, clinical, and hormonal parameters. MATERIALS AND METHODS: A cross-sectional study involving 69 PCOS women was carried out in a tertiary care center hospital. The diagnosis of PCOS was made according to the Rotterdam criteria. Blood samples were collected in the follicular phase of the menstrual cycle and analyzed for fasting luteinizing hormone (LH), follicle stimulating hormone (FSH), prolactin (PRL), 17-hydroxyprogesterone (17-OHP), total testosterone (T), glucose, insulin, and lipid profile. Urinary albumin was measured in the first void spot urine sample. RESULTS: The mean age of the subjects was 22.0 ± 4.1 years and 21.8 ± 4.7 years in normoalbuminuric and microalbuminuric groups, respectively. Urinary albumin excretion (UAE) varied from 5 mg/l to 100 mg/ml, with a median of 5 mg/l. Microalbuminuria was observed in 17/69 (24.6%) of subjects. The mean UAE was 3.65 ± 4.44 mg/l in the normoalbuminuria group versus 45.29 ± 22.74 mg/l in the microalbuminuria group. Upon univariate analysis, hip circumference, diastolic blood pressure, and fasting blood glucose showed significant correlations with urinary albumin concentration (r = 0.264, 0.264, and 0.551, respectively; P = 0.028, 0.029, and 0.000, respectively). No association between UAE and the usual cardiovascular risk factors could be found upon regression analysis. CONCLUSION: About 24.6% of women with PCOS showed presence of microalbuminuria in the first void spot urine sample. Screening for the presence of microalbuminuria can help in early identification of a subset of PCOS women with a high risk for future CVD, who can be subjected to preventive strategies at the earliest. However, further studies are needed before recommending routine use of UAE in PCOS cases for the detection of CVD risk.