scholarly journals Meta-analysis of QTLs associated with popping traits in maize (Zea mays L.)

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256389
Author(s):  
Sukhdeep Kaur ◽  
Sujay Rakshit ◽  
Mukesh Choudhary ◽  
Abhijit Kumar Das ◽  
Ranjeet Ranjan Kumar
Keyword(s):  
Carbohydrate Metabolism ◽  
Zea Mays L ◽  
Agronomic Traits ◽  
Meta Analysis ◽  
Physical Distance ◽  
Chromosome 1 ◽  
Gene Identification ◽  
Marker Assisted Breeding ◽  
Stalk Diameter ◽  
Reference Map

The rising demand for popcorn necessitates improving the popping quality with higher yield of popcorn cultivars. Towards this direction several Quantitative Traits Loci (QTLs) for popping traits have been identified. However, identification of accurate and consistent QTLs across different genetic backgrounds and environments is necessary to effectively utilize the identified QTLs in marker-assisted breeding. In the current study, 99 QTLs related to popping traits reported in 8 different studies were assembled and projected on the reference map "Genetic 2005" using BioMercator v4.2 to identify metaQTLs with consistent QTLs. Total ten metaQTLs were identified on chromosome 1 (7 metaQTLs) and 6 (3 metaQTLs) with physical distance ranging between 0.43 and 12.75 Mb, respectively. Four identified metaQTLs, viz., mQTL1_1, mQTL1_5, mQTL1_7 and mQTL6_2 harboured 5–8 QTL clusters with moderately high R2 value. The clustered QTLs were from two or more experiments. Based on the expression pattern in endosperm and pericarp tissues, a total of 229 genes were selected. Nineteen of these genes are involved in carbohydrate metabolism. Of the 19 genes specifically involved in carbohydrate metabolism, 11 of them were in these regions, implying the importance of these clustered QTLs. MetaQTL1_1 at bin location 1.01 coincided with the reported QTLs related to various agronomic traits like stalk diameter, tassel length, leaf area and plant height. The identified metaQTLs can be further explored for fine mapping and candidate gene identification, which can be validated by loss or gain of function. Identified metaQTLs can be used for introgression of popping traits towards enhancing the popping ability.

scholarly journals Selección para calidad fisiológica de la semilla y rendimiento en líneas S2 derivadas de cuatro poblaciones tropicales de maíz (Zea mays L.)

2016 ◽  
Vol 7 (1) ◽  
pp. 58
Author(s):  
Enrique Navarro ◽  
Cristina Vega ◽  
Fernando Narváez ◽  
Hugo Córdova
Keyword(s):  
Genetic Variability ◽  
Grain Yield ◽  
Recurrent Selection ◽  
Zea Mays L ◽  
Agronomic Traits ◽  
Reciprocal Recurrent Selection ◽  
Laboratory Conditions ◽  
Flower Plant ◽  
Ear Height ◽  
Field And Laboratory Conditions

This study was carried out in 1993 to evaluate S2 lines from four maize tropical populations improved by reciprocal recurrent selection. These lines were evaluated under field and laboratory conditions, the latter one to determine physiology quality. The main goal was to measure genetic variability within and among populations for traits such as grain yield, vigor and germination and to select the best lines under field and laboratory conditions. The combined analysis of variance showed great genetic variability among the S2 lines within and among populations for grain yield, days to flower, plant and ear height, among others. The maximum genetic variability was observed on the lines from population 43 and pool 23 for most of the traits, although the latter showed a greater genetic variability for grain yield. Besides, it is important to mention that the above populations included the best genotypes for grain yield, germination and vigor. Taking into account the above mentionel agronomic traits, fifteen lines were selected; 2 belong to population 43* pool 20, 2 from pool 19* pool 23, 8 from population 43, and 3 from pool 23. These results confirm the genetic superiority of the lines from populations 43 and pool 23, so that these populations should be recommended for future genetic improvement by reciprocal recurrent procedures.

Construction of genetic linkage map and identification of QTLs related to agronomic traits in DH population of maize (Zea mays L.) using SSR markers

2019 ◽  
Vol 41 (6) ◽  
pp. 667-678 ◽  
Author(s):  
Jae-Keun Choi ◽  
Kyu Jin Sa ◽  
Dae Hyun Park ◽  
Su Eun Lim ◽  
Si-Hwan Ryu ◽  
...  
Keyword(s):  
Zea Mays ◽  
Linkage Map ◽  
Ssr Markers ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Zea Mays L ◽  
Agronomic Traits ◽  
Dh Population

Comparison of teosinte (Zea mexicana L.) and inter-subspecific hybrids (Zea mays L.×Zea mexicana) for high forage yield under two sowing regimes

2015 ◽  
Vol 66 (1) ◽  
pp. 49 ◽  
Author(s):  
Imtiaz Akram Khan Niazi ◽  
Saeed Rauf ◽  
Jaime A. Teixeira da Silva ◽  
Hassan Munir
Keyword(s):  
Zea Mays ◽  
Heat Stress ◽  
Zea Mays L ◽  
Agronomic Traits ◽  
Plant Biomass ◽  
Stress Conditions ◽  
Forage Yield ◽  
Total Biomass ◽  
Percentage Survival ◽  
Biomass Plant

This study was undertaken to evaluate the response of teosinte (Zea mexicana L.) and intersubspecific hybrids to heat stress, in particular productivity. Unlike maize (Zea mays L.), teosinte demonstrated thermophilic properties, namely lower heat injury, sustained chlorophyll content under heat stress (36−45°C) and high percentage survival of seedlings (at 55°C). Teosinte also had the ability to produce large plant biomass (27% and 55% higher yield than maize under non-stressed and stress conditions, respectively) and therefore could be exploited as a forage crop. However, teosinte forage had low animal intake (1.48 kg day–1) because of high pubescence density (10.38 view–1) and low sweetness (9.90°Brix). There was a high percentage of heterosis in variable intersubspecific crosses and traits, and a high magnitude of over-dominance for many traits, for example 5.93–7.06 for total biomass plant–1. Hybrids showed additional advantages, including high oil (20% and 4%) and protein (14% and 25%) contents compared with teosinte under non-stressed and stress conditions, respectively. Moreover, inter-subspecific hybrids were also resistant to heat stress, with the capacity for sustaining growth for a longer period (20% and 33% higher than maize under non-stressed and stress conditions, respectively). Genetic distance between parents—calculated from stable agronomic traits—could be used to select parents for high heterosis under both heat stress and non-stressed conditions.

scholarly journals Genome-wide analysis of over 106 000 individuals identifies 9 neuroticism-associated loci

2016 ◽  
Vol 21 (6) ◽  
pp. 749-757 ◽  
Author(s):  
D J Smith ◽  
V Escott-Price ◽  
G Davies ◽  
M E S Bailey ◽  
L Colodro-Conde ◽  
...  
Keyword(s):  
Medical Research ◽  
Genetic Correlation ◽  
Meta Analysis ◽  
Small Sample ◽  
Chromosome 8 ◽  
Chromosome 17 ◽  
Chromosome 1 ◽  
Eysenck Personality Questionnaire ◽  
Uk Biobank ◽  
Genome Wide

Abstract Neuroticism is a personality trait of fundamental importance for psychological well-being and public health. It is strongly associated with major depressive disorder (MDD) and several other psychiatric conditions. Although neuroticism is heritable, attempts to identify the alleles involved in previous studies have been limited by relatively small sample sizes. Here we report a combined meta-analysis of genome-wide association study (GWAS) of neuroticism that includes 91 370 participants from the UK Biobank cohort, 6659 participants from the Generation Scotland: Scottish Family Health Study (GS:SFHS) and 8687 participants from a QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute (QIMR) cohort. All participants were assessed using the same neuroticism instrument, the Eysenck Personality Questionnaire-Revised (EPQ-R-S) Short Form’s Neuroticism scale. We found a single-nucleotide polymorphism-based heritability estimate for neuroticism of ∼15% (s.e.=0.7%). Meta-analysis identified nine novel loci associated with neuroticism. The strongest evidence for association was at a locus on chromosome 8 (P=1.5 × 10−15) spanning 4 Mb and containing at least 36 genes. Other associated loci included interesting candidate genes on chromosome 1 (GRIK3 (glutamate receptor ionotropic kainate 3)), chromosome 4 (KLHL2 (Kelch-like protein 2)), chromosome 17 (CRHR1 (corticotropin-releasing hormone receptor 1) and MAPT (microtubule-associated protein Tau)) and on chromosome 18 (CELF4 (CUGBP elav-like family member 4)). We found no evidence for genetic differences in the common allelic architecture of neuroticism by sex. By comparing our findings with those of the Psychiatric Genetics Consortia, we identified a strong genetic correlation between neuroticism and MDD and a less strong but significant genetic correlation with schizophrenia, although not with bipolar disorder. Polygenic risk scores derived from the primary UK Biobank sample captured ∼1% of the variance in neuroticism in the GS:SFHS and QIMR samples, although most of the genome-wide significant alleles identified within a UK Biobank-only GWAS of neuroticism were not independently replicated within these cohorts. The identification of nine novel neuroticism-associated loci will drive forward future work on the neurobiology of neuroticism and related phenotypes.

scholarly journals Physical and Genetic Mapping in the GrassesLolium perenneandFestuca pratensis

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 315-324 ◽  
Author(s):  
J King ◽  
I P Armstead ◽  
I S Donnison ◽  
H M Thomas ◽  
R N Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Physical Map ◽  
Rice Chromosome ◽  
Nucleolar Organizer ◽  
Physical Distance ◽  
Chromosome 1 ◽  
Grass Species ◽  
Nucleolar Organizer Regions ◽  
Single Chromosome ◽  
Large Scale Analysis

AbstractA single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line (2n = 2x = 14). In this line recombination occurs throughout the length of the F. pratensis/L. perenne bivalent. The F. pratensis chromosome and recombinants between it and its L. perenne homeologue can be visualized using genomic in situ hybridization (GISH). GISH junctions represent the physical locations of sites of recombination, enabling a range of recombinant chromosomes to be used for physical mapping of the introgressed F. pratensis chromosome. The physical map, in conjunction with a genetic map composed of 104 F. pratensis-specific amplified fragment length polymorphisms (AFLPs), demonstrated: (1) the first large-scale analysis of the physical distribution of AFLPs; (2) variation in the relationship between genetic and physical distance from one part of the F. pratensis chromosome to another (e.g., variation was observed between and within chromosome arms); (3) that nucleolar organizer regions (NORs) and centromeres greatly reduce recombination; (4) that coding sequences are present close to the centromere and NORs in areas of low recombination in plant species with large genomes; and (5) apparent complete synteny between the F. pratensis chromosome and rice chromosome 1.

scholarly journals Association analysis of genes involved in maize (Zea mays L.) root development with seedling and agronomic traits under contrasting nitrogen levels

2015 ◽  
Vol 88 (1-2) ◽  
pp. 133-147 ◽  
Author(s):  
Adel H. Abdel-Ghani ◽  
Bharath Kumar ◽  
Jordon Pace ◽  
Constantin Jansen ◽  
Pedro J. Gonzalez-Portilla ◽  
...  
Keyword(s):  
Zea Mays ◽  
Association Analysis ◽  
Root Development ◽  
Zea Mays L ◽  
Agronomic Traits ◽  
Nitrogen Levels

scholarly journals Assembly of chromosome-scale and allele-aware autotetraploid genome of the Chinese alfalfa cultivar Zhongmu-4 and identification of SNP loci associated with 27 agronomic traits

2021 ◽  
Author(s):  
Ruicai Long ◽  
Fan Zhang ◽  
Zhiwu Zhang ◽  
Mingna Li ◽  
Lin Chen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Agronomic Traits ◽  
Association Studies ◽  
Genetic Research ◽  
Chromosome 1 ◽  
Genome Wide Association Studies ◽  
Forage Crops ◽  
Legume Crop ◽  
Population Structure Analysis

AbstractAlfalfa (Medicago sativaL.), the most valuable perennial legume crop, referred to as “Queen of the Forages” for its high nutritional value and yield production among forage crops. Comprehensive genomic information of germplasm resources from different ecological regions and modern breeding strategies, such as molecular-marker assisted breeding are of great importance to breed new alfalfa varieties with environmental resilience. Here, we report assembly of the genome sequence of Zhongmu-4 (ZM-4), one of the most planted cultivars in China, and identification of SNPs associated with alfalfa agronomic traits by Genome-wide Association Studies (GWAS). Sequence of 32 allelic chromosomes was assembled successfully by single molecule real time sequencing and Hi-C technique with ALLHiC algorithm. About 2.74 Gbp contigs, accounting for 88.39% of the estimated genome, were assembled with 2.56 Gbp contigs anchored to 32 pseudo-chromosomes. In comparison withM. truncatulaA17, distinctive inversion and translocation on chromosome 1, and between chromosome 4 and 8, respectively, were detected. Moreover, we conducted resequencing of 220 alfalfa accessions collected globally and performed GWAS analysis based on our assembled genome. Population structure analysis demonstrated that alfalfa has a complex genetic relationship among germplasm with different geographic origins. GWAS identified 101 SNPs associated with 27 out of 93 agronomic traits. The updated chromosome-scale and allele-aware genome sequence, coupled with the resequencing data of most global alfalfa germplasm, provides valuable information for alfalfa genetic research, and further analysis of major SNP loci will accelerate unravelling the molecular basis of important agronomic traits and facilitate genetic improvement of alfalfa.

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