Meta-QTL analysis and identification of candidate genes related to root traits in maize

Euphytica ◽  
2018 ◽  
Vol 214 (12) ◽  
Author(s):  
Jian Guo ◽  
Lin Chen ◽  
Yongxiang Li ◽  
Yunsu Shi ◽  
Yanchun Song ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Qtl Analysis ◽  
Root Traits

scholarly journals Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jose Miguel Soriano ◽  
Pasqualina Colasuonno ◽  
Ilaria Marcotuli ◽  
Agata Gadaleta
Keyword(s):  
Molecular Markers ◽  
Abiotic Stress ◽  
Durum Wheat ◽  
Candidate Genes ◽  
Biotic Stress ◽  
Qtl Analysis ◽  
Complex Traits ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

scholarly journals Identification of Candidate Gene for Internode Length in Rice to Enhance Resistance to Lodging Using QTL Analysis

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1369
Author(s):  
Dan-Dan Zhao ◽  
Ju-Hyeong Son ◽  
Muhammad Farooq ◽  
Kyung-Min Kim
Keyword(s):  
Candidate Genes ◽  
Qtl Analysis ◽  
Middle Part ◽  
Internode Length ◽  
Stem Diameter ◽  
Chromosome 1 ◽  
Doubled Haploid Population ◽  
Lodging Resistance ◽  
Cytochrome P450 Family ◽  
Uppermost Internode

Internode length and stem diameter are the primary traits affecting the lodging resistance of rice. Traits related to the length of the panicle (LP), uppermost internode (LUI), second internode (LSI), third internode (LTI), fourth internode (LFI), lowest internode (LLI) as well as stem diameter at the uppermost internode (SDUI), second internode (SDSI), third internode (SDTI), fourth internode (SDFI), and lowest internode (SDLI) in 120 Cheongcheong/Nagdong doubled haploid population were investigated using a quantitative trait locus (QTL) analysis. Thirty-four QTL regions affected LP and the length of each internode. Twenty-six QTL regions were associated with the stem diameter of each internode. RM12285-RM212 on chromosome 1 contained 10 QTLs related to the internode length, which have overlapped for over 2 years. Twenty-three candidate genes were screened using mark interval. Among the candidate genes, Os01g0803900, named OsCYPq1, which is in the Cytochrome P450 family, might be involved in gibberellins (GA) synthesis. GA is an essential plant growth regulator that affects plant height. OsCYPq1 catalyzes oxidation steps in the middle part of the GA pathway. OsCYPq1 is expected to provide valuable information to improve the marker assessment for target traits and QTL gene cloning in rice.

scholarly journals Genetic dissection of aroma volatile compounds from the essential oil of peach fruit: QTL analysis and identification of candidate genes using dense SNP maps

2012 ◽  
Vol 9 (1) ◽  
pp. 189-204 ◽  
Author(s):  
Iban Eduardo ◽  
Giorgiana Chietera ◽  
Raul Pirona ◽  
Igor Pacheco ◽  
Michela Troggio ◽  
...  
Keyword(s):  
Essential Oil ◽  
Volatile Compounds ◽  
Candidate Genes ◽  
Qtl Analysis ◽  
Genetic Dissection ◽  
Peach Fruit

scholarly journals Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean (Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity

2021 ◽  
Vol 12 ◽  
Author(s):  
Daniel Ambachew ◽  
Matthew W. Blair
Keyword(s):  
Common Bean ◽  
Candidate Genes ◽  
Aluminum Toxicity ◽  
Root Traits ◽  
Al Toxicity ◽  
Genome Wide Association ◽  
Soil Conditions ◽  
Polygenic Inheritance ◽  
Genome Wide ◽  
Significant Difference

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed.

scholarly journals Meta-QTL analysis and identification of candidate genes for drought tolerance in bread wheat (Triticum aestivum L.)

2020 ◽  
Vol 26 (8) ◽  
pp. 1713-1725
Author(s):  
Anuj Kumar ◽  
Gautam Saripalli ◽  
Irfat Jan ◽  
Kuldeep Kumar ◽  
P. K. Sharma ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Drought Tolerance ◽  
Candidate Genes ◽  
Bread Wheat ◽  
Qtl Analysis ◽  
Triticum Aestivum L

scholarly journals Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 773 ◽  
Author(s):  
Wang ◽  
Wei ◽  
Li ◽  
Wang ◽  
Ge ◽  
...  
Keyword(s):  
Root System ◽  
Candidate Genes ◽  
Root Development ◽  
Root Length ◽  
Root Traits ◽  
Root Surface ◽  
Root Surface Area ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Short Root

Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of 13 root and 3 shoot traits was evaluated in 297 maize inbred lines and genome-wide association mapping was conducted to identify SNPs associated with target traits. All measured traits exhibited 2.02- to 21.36-fold variations. A total of 34 quantitative trait loci (QTLs) were detected for 13 traits, and each individual QTL explained 5.7% to 15.9% of the phenotypic variance. Three pleiotropic QTLs involving five root traits were identified; SNP_2_104416607 was associated with lateral root length (LRL), root surface area (RA), root length between 0 and 0.5mm in diameter (RL005), and total root length (TRL); SNP_2_184016997 was associated with RV and RA, and SNP_4_168917747 was associated with LRL, RA and TRL. The expression levels of candidate genes in root QTLs were evaluated by RNA-seq among three long-root lines and three short-root lines. A total of five genes that showed differential expression between the long- and short-root lines were identified as promising candidate genes for the target traits. These QTLs and the potential candidate genes are important source data to understand root development and genetic improvement of root traits in maize.

Identifying drought-resilient flax genotypes and related-candidate genes based on stress indices, root traits and selective sweep

Euphytica ◽  
2019 ◽  
Vol 215 (3) ◽  
Author(s):  
Braulio J. Soto-Cerda ◽  
Sylvie Cloutier ◽  
Humberto A. Gajardo ◽  
Gabriela Aravena ◽  
Rocio Quian
Keyword(s):  
Candidate Genes ◽  
Selective Sweep ◽  
Root Traits ◽  
Stress Indices

scholarly journals Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 367 ◽  
Author(s):  
Siriluck Ponsuksili ◽  
Elisabeth Jonas ◽  
Eduard Murani ◽  
Chirawath Phatsara ◽  
Tiranun Srikanchai ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Qtl Analysis ◽  
Biological Pathways ◽  
Water Holding Capacity ◽  
Expression Qtl ◽  
Water Holding
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