scholarly journals Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.)

2021 ◽  
Author(s):  
Joshua N. Cobb ◽  
Chen Chen ◽  
Yuxin Shi ◽  
Lyza G. Maron ◽  
Danni Liu ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Candidate Genes ◽  
Association Analysis ◽  
Phenotypic Variation ◽  
Genetic Variants ◽  
Genetic Basis ◽  
Living Environment ◽  
Mineral Nutrient ◽  
Genome Wide ◽  
Genomic Regions

Abstract Key message Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Abstract Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.

scholarly journals Genome-Wide Association Studies of Leaf Angle in Maize

2021 ◽  
Author(s):  
Bo Peng ◽  
Xiaolei Zhao ◽  
Yi Wang ◽  
Chunhui Li ◽  
Yongxiang Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association ◽  
Leaf Angle ◽  
Genome Wide Association Studies ◽  
Major Qtls ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
A Genome

Abstract Compact plant-type with small leaf angle has increased canopy light interception, which is conducive to the photosynthesis of the population and higher population yield at high density planting in maize. In this study, a panel of 285 diverse maize inbred lines genotyped with 56,000 SNPs was used to investigate the genetic basis of leaf angle across three consecutive years using a genome-wide association study (GWAS). The leaf angle showed broad phenotypic variation and high heritability across different years. Population structure analysis subdivided the panel into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Tangsipingtou, Reid, Lancaster and P. When tested with the optimal GWAS model, we found that the Q+K model was the best in reducing false positive. In total, 96 SNPs accounting for 5.54%-10.44% of phenotypic variation were significantly (P<0.0001) associated with leaf angle across three years. According to the linkage disequilibrium decay distance, 96 SNPs were binned in 43 QTLs for leaf angle. Seven major QTLs with R2>8% stably detected in at least two years and BLUP values were clustered in four genomic regions (bins 2.01, 2.07, 5.06, and 10.04). Seven important candidate genes, Zm00001d001961, Zm00001d006348, Zm00001d006463, Zm00001d017618, Zm00001d024919, Zm00001d025018, and Zm00001d025033 were predicted for the seven stable major QTLs, respectively. The markers identified in this study can be used for molecular breeding for leaf angle, and the candidate genes would contribute to further understanding of the genetic basis of leaf angle.

scholarly journals Genomic regions controlling shape variation in the first upper molar of the house mouse

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Luisa F Pallares ◽  
Ronan Ledevin ◽  
Sophie Pantalacci ◽  
Leslie M Turner ◽  
Eirikur Steingrimsson ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Shape Variation ◽  
Tooth Shape ◽  
Mus Musculus Musculus ◽  
Genome Wide ◽  
Genomic Regions ◽  
Hybrid Mice ◽  
Upper Molar

Numerous loci of large effect have been shown to underlie phenotypic variation between species. However, loci with subtle effects are presumably more frequently involved in microevolutionary processes but have rarely been discovered. We explore the genetic basis of shape variation in the first upper molar of hybrid mice between Mus musculus musculus and M. m. domesticus. We performed the first genome-wide association study for molar shape and used 3D surface morphometrics to quantify subtle variation between individuals. We show that many loci of small effect underlie phenotypic variation, and identify five genomic regions associated with tooth shape; one region contained the gene microphthalmia-associated transcription factor Mitf that has previously been associated with tooth malformations. Using a panel of five mutant laboratory strains, we show the effect of the Mitf gene on tooth shape. This is the first report of a gene causing subtle but consistent variation in tooth shape resembling variation in nature.

scholarly journals Uncovering Novel Genomic Regions and Candidate Genes for Senescence-Related Traits by Genome-Wide Association Studies in Upland Cotton (Gossypium hirsutum L.)

2022 ◽  
Vol 12 ◽  
Author(s):  
Qibao Liu ◽  
Libei Li ◽  
Zhen Feng ◽  
Shuxun Yu
Keyword(s):  
Candidate Genes ◽  
Upland Cotton ◽  
Genetic Basis ◽  
Association Studies ◽  
White Flower ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
High Positive Correlation ◽  
Genome Wide ◽  
Genomic Regions

Senescence in plants is a complex trait, which is controlled by both genetic and environmental factors and can affect the yield and quality of cotton. However, the genetic basis of cotton senescence remains relatively unknown. In this study, we reported genome-wide association studies (GWAS) based on 185 accessions of upland cotton and 26,999 high-quality single-nucleotide polymorphisms (SNPs) to reveal the genetic basis of cotton senescence. To determine cotton senescence, we evaluated eight traits/indices. Our results revealed a high positive correlation (r&gt;0.5) among SPAD value 20 days after topping (SPAD20d), relative difference of SPAD (RSPAD), nodes above white flower on topping day (NAWF0d), nodes above white flower 7 days after topping (NAWF7d), and number of open bolls on the upper four branches (NB), and genetic analysis revealed that all traits had medium or high heritability ranging from 0.53 to 0.86. Based on a multi-locus method (FASTmrMLM), a total of 63 stable and significant quantitative trait nucleotides (QTNs) were detected, which represented 50 genomic regions (GWAS risk loci) associated with cotton senescence. We observed three reliable loci located on chromosomes A02 (A02_105891088_107196428), D03 (D03_37952328_38393621) and D13 (D13_59408561_60730103) because of their high repeatability. One candidate gene (Ghir_D03G011060) was found in the locus D03_37952328_38393621, and its Arabidopsis thaliana homologous gene (AT5G23040) encodes a cell growth defect factor-like protein (CDF1), which might be involved in chlorophyll synthesis and cell death. Moreover, qRT-PCR showed that the transcript level of Ghir_D03G011060 was down-regulated in old cotton leaves, and virus-induced gene silencing (VIGS) indicated that silencing of Ghir_D03G011060 resulted in leaf chlorosis and promoted leaf senescence. In addition, two candidate genes (Ghir_A02G017660 and Ghir_D13G021720) were identified in loci A02_105891088_107196428 and D13_59408561_60730103, respectively. These results provide new insights into the genetic basis of cotton senescence and will serve as an important reference for the development and implementation of strategies to prevent premature senescence in cotton breeding programs.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P &lt; 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

scholarly journals Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 718
Author(s):  
Bingxin Meng ◽  
Tao Wang ◽  
Yi Luo ◽  
Deze Xu ◽  
Lanzhi Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Genome Wide Association ◽  
Lodging Resistance ◽  
Leaf Type ◽  
Stem Strength ◽  
Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

scholarly journals Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

2021 ◽  
Vol 22 (7) ◽  
pp. 3477
Author(s):  
Julia Zaborowska ◽  
Bartosz Łabiszak ◽  
Annika Perry ◽  
Stephen Cavers ◽  
Witold Wachowiak
Keyword(s):  
Population Structure ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Redox Homeostasis ◽  
Snp Markers ◽  
Regulation Of Transcription ◽  
Single Nucleotide ◽  
Homeostasis Regulation ◽  
Genomic Regions ◽  
Mountain Plants

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

Sign in / Sign up

Export Citation Format

Share Document