Genomic regions associated with salinity stress tolerance in tropical maize (Zea Mays L.)

Being a widely cultivated crop globally under diverse climatic conditions and soil types, maize is often exposed to an array of biotic and abiotic stresses. Soil salinity is one of the challenges for maize cultivation in many parts of lowland tropics that significantly affects crop growth and reduces economic yields. Breeding strategies integrated with molecular approach might accelerate the process of identifying and developing salinity-tolerant maize cultivars. In this study, an association mapping panel consisting of 305 diverse maize inbred lines was phenotyped in a managed salinity stress phenotyping facility at International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates (UAE). Wide genotypic variability was observed in the panel under salinity stress for key phenotypic traits viz., grain yield, days to anthesis, anthesis-silking interval, plant height, cob length, cob girth, and kernel number. The panel was genotyped following the genome-based sequencing approach to generate 955,690 SNPs. Total SNPs were filtered to 213,043 at a call rate of 0.85 and minor allele frequency of 0.05 for association analysis. A total of 259 highly significant (P ≤ 1 × 10–5) marker-trait associations (MTAs) were identified for seven phenotypic traits. The phenotypic variance for MTAs ranged between 5.2 and 9%. A total of 64 associations were found in 19 unique putative gene expression regions. Among them, 12 associations were found in gene models with stress-related biological functions

Contribution of root system architecture and function in the performance of tropical maize (Zea mays L.) genotypes under different moisture regimes

Understanding how roots respond to increasing rate of evapotranspiration in warmer days and exposure to dry spells is crucial for saving productivity of rainfed crops, including maize, grown in Asian tropics. In a semi-automatic root phenotyping facility (lysimetric system) a set of 100 elite and diverse tropical maize inbred lines were phenotyped under managed drought stress (DT) and well-watered (WW) conditions. Plants were grown in PVC (Polyvinyl chloride) cylinder of 30.0 cm diameter and 150.0 cm length. In drought experiment, last irrigation was applied based accumulated growing degree days (∑GDD) criteria to achieved reproductive stress DT, whereas optimal moisture was maintained in WW trials. Data recorded on various root structural and function traits in both DT and WW trials. Significant phenotypic variability was observed for various root traits, including both structural and functional traits, under both the moisture regimes. Correlation studies showed that grain yield of early maturity group of genotypes was positively and significantly associated with all the root structural traits under drought, whereas, in case of medium and late maturity group of entries root structural traits showed either weak positive or significant negative correlation with grain yield under drought. Though, root functional traits of all the maturity group of genotypes showed positive and significant correlations with both grain yield and total biomass under both well-watered drought stress. Regression analysis showed that water uptake had significant positive relationship with total biomass in all the three-maturity group of genotypes. However, grain yield seems to be less dependent directly on the total amount of water uptake. We conclude that contribution of various traits in root system architecture under drought or well-watered conditions vary with maturity of genotypes. However, root functional traits, such as water uptake and transpiration efficiency are equally important across maturity groups and water availability regimes

Karachi cancer registry (KCR): Age-standardized incidence rate by age-group and gender in a mega city of Pakistan

Objectives: To estimate the cancer incidence by age group and gender for the population of Karachi Division by analyzing the Karachi Cancer Registry data of 2017-19.Settings: The population of Karachi division is 16.1 million according to national census 2017. \u27Karachi Cancer Registry\u27 which is a part of \u27National Cancer Registry\u27 is collecting data from eight major hospitals in Karachi since 2017. For outcome measures, cancer counts and the age standardized incidence rates (ASIR) per 100,000 population were computed for age groups (0-14, 15-19 and ≥20 years), in both genders and all cancer site/type.Methods: The population denominators were based on the population of Karachi division estimated at 16.1 million in the population census, 2017. Counts and age-standardized incidence rates (ASIR) were calculated for each of the three age categories.Results: From Jan 2017 till Dec 2019 a total of 33,309 malignant cases were recorded in KCR database comprising 17,490 (52.5%) females and 15,819 (47.5%) males. ASIRs in age groups 0-14, 15-19 and ≥ 20 years, among female were 11.5, 2.4 and 223.6 and in males were 17.6, 3.2 and 216.7 respectively. The commonest diagnosis in children, adolescent and adults were (1) among females: children; bone (3.12), leukemia (2.09) brain/CNS (1.26); in adolescents: bone (0.78), brain/CNS (0.27), connective and soft tissue (0.11), in adults: breast cancer (76.07), oral cancer (16.68) and ovary (10.89) respectively, and (2) among males: children; bone (4.56), leukemia (2.79) and brain/CNS (1.88); in adolescent; bone (1.19), brain/CNS (0.31) and leukemia (0.21) and in adults: oral cancer (42.83), liver (16.10) and bone (13.37) respectively.Conclusion: Oral Cancer, a largely preventable cancer is the leading cancer in Karachi adult males while in female adults Breast Cancer is the leading cancer followed by Oral Cancer. In children and adolescents Bone, Leukemia and Brain/CNS malignancies are most common.

Genetic trends in CIMMYT’s tropical maize breeding pipelines

Fostering a culture of continuous improvement through regular monitoring of genetic trends in breeding pipelines is essential to improve efficiency and increase accountability. This is the first global study to estimate genetic trends across the International Maize and Wheat Improvement Center (CIMMYT) tropical maize breeding pipelines in eastern and southern Africa (ESA), South Asia, and Latin America over the past decade. Data from a total of 4152 advanced breeding trials and 34,813 entries, conducted at 1331 locations in 28 countries globally, were used for this study. Genetic trends for grain yield reached up to 138 kg ha−1 yr−1 in ESA, 118 kg ha−1 yr−1 South Asia and 143 kg ha−1 yr−1 in Latin America. Genetic trend was, in part, related to the extent of deployment of new breeding tools in each pipeline, strength of an extensive phenotyping network, and funding stability. Over the past decade, CIMMYT’s breeding pipelines have significantly evolved, incorporating new tools/technologies to increase selection accuracy and intensity, while reducing cycle time. The first pipeline, Eastern Africa Product Profile 1a (EA-PP1a), to implement marker-assisted forward-breeding for resistance to key diseases, coupled with rapid-cycle genomic selection for drought, recorded a genetic trend of 2.46% per year highlighting the potential for deploying new tools/technologies to increase genetic gain

QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

AbstractWaterlogging is an important abiotic stress constraint that causes significant yield losses inmaize grown throughout south and south-east Asia due to erratic rainfall patterns. The mosteconomic option to offset the damage caused by waterlogging is to genetically incorporatetolerance in cultivars that are grown widely in the target agro-ecologies. We assessed thegenetic variation in a population of recombinant inbred lines (RILs) derived from crossing awaterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) andobserved significant range of variation for grain yield (GY) under waterlogging stress alongwith a number of other secondary traits such as brace roots (BR), chlorophyll content(SPAD), %stem and root lodging (S&RL) among the RILs. Significant positive correlation ofGY with BR and SPAD and negative correlation with S&RL indicated the potential use ofthese secondary traits in selection indices under waterlogged conditions. RILs were genotypedwith 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP(Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variancefor GY based on evaluation of RIL families under waterlogged conditions, with effectsranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for varioussecondary traits associated with waterlogging tolerance, each individually explainingfrom 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domainsidentified within the physical intervals delimited by the flanking markers of the QTLinfluencing GY and other secondary traits, six have previously been demonstrated to be associatedwith anaerobic responses in either maize or other model species. A pair of flankingSNP markers has been identified for each of the QTL and high throughput marker assayswere developed to facilitate rapid introgression of waterlogging tolerance in tropical maizebreeding programs

Genome wide association mapping for heat tolerance in sub-tropical maize

Not AvailableHeat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollination failure and barren ears that causes devastating yield losses. So, there is need to identify the genomic regions associated with heat tolerance component traits which could be further employed in maize breeding program.An association mapping panel, consisting of 662 doubled haploid (DH) lines, was evaluated for yield contributing traits under normal and natural heat stress conditions. Genome wide association studies (GWAS) carried out using 187,000 SNPs and 130 SNPs significantly associated for grain yield (GY), days to 50% anthesis (AD), days to 50% silking (SD), anthesis-silking interval (ASI), plant height (PH), ear height (EH) and ear position (EPO) were identified under normal conditions. A total of 46 SNPs strongly associated with GY, ASI, EH and EPO were detected under heat stress conditions. Fifteen of the SNPs was found to have common association with more than one trait such as two SNPs viz. S10_1,905,273 and S10_1,905,274 showed colocalization with GY, PH and EH whereas S10_7,132,845 SNP associated with GY, AD and SD under normal conditions. No such colocalization of SNP markers with multiple traits was observed under heat stress conditions. Haplotypes trend regression analysis revealed 122 and 85 haplotype blocks, out of which, 20 and 6 haplotype blocks were associated with more than one trait under normal and heat stress conditions, respectively. Based on SNP association and haplotype mapping, nine and seven candidate genes were identified respectively, which belongs to different gene models having different biological functions in stress biology. The present study identified significant SNPs and haplotype blocks associated with yield contributing traits that help in selection of donor lines with favorable alleles for multiple traits. These results provided insights of genetics of heat stress tolerance. The genomic regions detected in the present study need further validation before being applied in the breeding pipelines.Not Availabl

QTL identified for waterlogging tolerance using RIL phenotypes.

<p>QTL identified for waterlogging tolerance using RIL phenotypes.</p