Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior

Abstract Melon is as an alternative model to understand fruit ripening due to the coexistence of climacteric and non-climacteric varieties within the same species, allowing the study of the processes that regulate this complex trait with genetic approaches. We phenotyped a population of recombinant inbred lines (RILs), obtained by crossing a climacteric (Védrantais, cantalupensis type) and a non-climcteric variety (Piel de Sapo T111, inodorus type), for traits related to climacteric maturation and ethylene production. Individuals in the RIL population exhibited various combinations of phenotypes that differed in the amount of ethylene produced, the early onset of ethylene production, and other phenotypes associated with ripening. We characterized a major QTL on chromosome 8, ETHQV8.1, which is sufficient to activate climacteric ripening, and other minor QTLs that may modulate the climacteric response. The ETHQV8.1 allele was validated by using two reciprocal introgression line populations generated by crossing Védrantais and Piel de Sapo and analyzing the ETHQV8.1 region in each of the genetic backgrounds. A Genome-wide association study (GWAS) using 211 accessions of the ssp. melo further identified two regions on chromosome 8 associated with the production of aromas, one of these regions overlapping with the 154.1 kb interval containing ETHQV8.1. The ETHQV8.1 region contains several candidate genes that may be related to fruit ripening. This work sheds light into the regulation mechanisms of a complex trait such as fruit ripening.

Download Full-text

Genetic Dissection of Temperament Personality Traits in Italian Isolates

Genes ◽

10.3390/genes13010004 ◽

2021 ◽

Vol 13 (1) ◽

pp. 4

Author(s):

Maria Pina Concas ◽

Alessandra Minelli ◽

Susanna Aere ◽

Anna Morgan ◽

Paola Tesolin ◽

...

Keyword(s):

Genome Wide Association Study ◽

Complex Trait ◽

Domestic Dog ◽

P Value ◽

Genetic Dissection ◽

Novelty Seeking ◽

Obsessive Compulsive ◽

Compulsive Disorder ◽

New Genes ◽

A Genome

Human personality (i.e., temperament and character) is a complex trait related to mental health, influenced by genetic and environmental factors. Despite the efforts performed during the past decades, its genetic background is only just beginning to be identified. With the aim of dissecting the genetic basis of temperament, we performed a Genome-Wide Association Study (GWAS) on Cloninger’s Temperament and Character Inventory in 587 individuals belonging to different Italian genetic isolates. Data analysis led to the identification of four new genes associated with different temperament scales, such as Novelty Seeking (NS), Harm Avoidance (HA), and Reward Dependence (RD). In detail, we identified suggestive and significant associations between: MAGI2 (highest p-value = 9.14 × 10−8), a gene already associated with schizophrenia and depressive disorder, and the NS–Extravagance scale; CALCB (highest p-value = 4.34 × 10−6), a gene likely involved in the behavioral evolution from wild wolf to domestic dog, and the NS–Disorderliness scale; BTBD3 (highest p-value = 2.152 × 10−8), a gene already linked to obsessive–compulsive disorder, and the HA–Fatigability scale; PRKN (highest p-value = 8.27 × 10−9), a gene described for early onset Parkinson’s disease, and the RD scale. Our work provides new relevant insights into the genetics of temperament, helping to elucidate the molecular basis of psychiatric disorders.

Download Full-text

Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models

Scientific Reports ◽

10.1038/s41598-021-86127-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ali Muhammad ◽

Jianguo Li ◽

Weichen Hu ◽

Jinsheng Yu ◽

Shahid Ullah Khan ◽

...

Keyword(s):

Plant Height ◽

Genome Wide Association Study ◽

Flag Leaf ◽

Significant Snps ◽

Complex Trait ◽

Leaf Length ◽

Candidate Snps ◽

A Genome ◽

Multiple Environments ◽

Architectural Traits

AbstractWheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.

Download Full-text

GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1904964116 ◽

2019 ◽

Vol 116 (42) ◽

pp. 21262-21267 ◽

Cited By ~ 22

Author(s):

Kenji Yano ◽

Yoichi Morinaka ◽

Fanmiao Wang ◽

Peng Huang ◽

Sayaka Takehara ◽

...

Keyword(s):

Principal Component Analysis ◽

Genome Wide Association Study ◽

Crop Yields ◽

Principal Component ◽

Complex Trait ◽

Component Analysis ◽

Gene Encoding ◽

Signal Suppression ◽

Genome Wide ◽

A Genome

Elucidation of the genetic control of rice architecture is crucial due to the global demand for high crop yields. Rice architecture is a complex trait affected by plant height, tillering, and panicle morphology. In this study, principal component analysis (PCA) on 8 typical traits related to plant architecture revealed that the first principal component (PC), PC1, provided the most information on traits that determine rice architecture. A genome-wide association study (GWAS) using PC1 as a dependent variable was used to isolate a gene encoding rice, SPINDLY (OsSPY), that activates the gibberellin (GA) signal suppression protein SLR1. The effect of GA signaling on the regulation of rice architecture was confirmed in 9 types of isogenic plant having different levels of GA responsiveness. Further population genetics analysis demonstrated that the functional allele of OsSPY associated with semidwarfism and small panicles was selected in the process of rice breeding. In summary, the use of PCA in GWAS will aid in uncovering genes involved in traits with complex characteristics.

Download Full-text

Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study

Journal of Experimental Botany ◽

10.1093/jxb/eru419 ◽

2014 ◽

Vol 66 (1) ◽

pp. 293-306 ◽

Cited By ~ 38

Author(s):

Yoshiaki Ueda ◽

Felix Frimpong ◽

Yitao Qi ◽

Elsa Matthus ◽

Linbo Wu ◽

...

Keyword(s):

Oryza Sativa ◽

Association Study ◽

Genome Wide Association Study ◽

Oryza Sativa L ◽

Genome Wide Association ◽

Genetic Dissection ◽

Genome Wide ◽

A Genome ◽

Ozone Tolerance

Download Full-text

Heterotaxy in Caenorhabditis : widespread natural variation in left–right arrangement of the major organs

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0404 ◽

2016 ◽

Vol 371 (1710) ◽

pp. 20150404 ◽

Cited By ~ 5

Author(s):

Melissa R. Alcorn ◽

Davon C. Callander ◽

Agustín López-Santos ◽

Yamila N. Torres Cleuren ◽

Bilge Birsoy ◽

...

Keyword(s):

Genome Wide Association Study ◽

Recombinant Inbred Lines ◽

Sensitive Period ◽

Temperature Sensitive ◽

Internal Organs ◽

Genome Wide ◽

A Genome ◽

Natural Isolates ◽

Left Right Asymmetry ◽

Genomic Regions

Although the arrangement of internal organs in most metazoans is profoundly left–right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematode Caenorhabditis elegans is known for its highly determinate development, including stereotyped L/R organ handedness, we found that L/R asymmetry of the major organs, the gut and gonad, varies among natural isolates of the species in both males and hermaphrodites. In hermaphrodites, heterotaxy can involve one or both bilaterally asymmetric gonad arms. Male heterotaxy is probably not attributable to relaxed selection in this hermaphroditic species, as it is also seen in gonochoristic Caenorhabditis species. Heterotaxy increases in many isolates at elevated temperature, with one showing a pregastrulation temperature-sensitive period, suggesting a very early embryonic or germline effect on this much later developmental outcome. A genome-wide association study of 100 isolates showed that male heterotaxy is associated with three genomic regions. Analysis of recombinant inbred lines suggests that a small number of loci are responsible for the observed variation. These findings reveal that heterotaxy is a widely varying quantitative trait in an animal with an otherwise highly stereotyped anatomy, demonstrating unexpected plasticity in an L/R arrangement of the major organs even in a simple animal. This article is part of the themed issue ‘Provocative questions in left–right asymmetry’.

Download Full-text

Identification of a Gene Encoding Glutamate Decarboxylase Involved in the Postharvest Fruit Ripening Process in Banana

HortScience ◽

10.21273/hortsci.49.8.1056 ◽

2014 ◽

Vol 49 (8) ◽

pp. 1056-1060 ◽

Cited By ~ 4

Author(s):

Wei Hu ◽

Ju-Hua Liu ◽

Xiao-Ying Yang ◽

Jian-Bin Zhang ◽

Cai-Hong Jia ◽

...

Keyword(s):

Fruit Ripening ◽

Ethylene Production ◽

Glutamate Decarboxylase ◽

Ethylene Biosynthesis ◽

Gene Encoding ◽

Ripening Process ◽

Climacteric Fruit ◽

Genes Encoding ◽

Postharvest Ripening ◽

Exogenous Ethylene

The banana, a typical climacteric fruit, undergoes a postharvest ripening process followed by a burst in ethylene production that signals the beginning of the climacteric period. Postharvest ripening plays an important role in improving the quality of the fruit as well as limiting its shelf life. To investigate the role of glutamate decarboxylase (GAD) in climacteric ethylene biosynthesis and fruit ripening in postharvest banana, a GAD gene was isolated from banana, designated MuGAD. Coincidently with climacteric ethylene production, MuGAD expression as well as the expression of the genes encoding the Musa 1-aminocyclopropane-1-carboxylate synthase (MaACS1) and Musa 1-aminocyclopropane-1-carboxylate oxidase (MaACO1) greatly increased during natural ripening and in ethylene-treated banana. Moreover, ethylene biosynthesis, ripening progress, and MuGAD, MaACS1, and MaACO1 expression were enhanced by exogenous ethylene application and inhibited by 1-methylcyclopropene (1-MCP). Taken together, our results suggested that MuGAD is involved in the fruit ripening process in postharvest banana.

Download Full-text

Effect of 1-MCP on Apple Fruit Ripening and Volatile Production

HortScience ◽

10.21273/hortsci.32.3.536d ◽

1997 ◽

Vol 32 (3) ◽

pp. 536D-536 ◽

Cited By ~ 8

Author(s):

J. Song ◽

M.S. Tian ◽

D.R. Dilley ◽

R.M. Beaudry

Keyword(s):

Fruit Ripening ◽

Ethylene Production ◽

Quality Criterion ◽

Apple Fruit ◽

Climacteric Fruit ◽

Aroma Production ◽

Ethylene Action ◽

Important Quality ◽

The Relationship ◽

Volatile Production

Aroma production by apple fruit is an important quality criterion and has been found to be a fruit-ripening-related process. 1-Methylcyclopropene (1-MCP), an effective ethylene action inhibitor, was used to study the relationship between volatile biosynthesis, ethylene action, and fruit ripening in `Golden Delicious' apple fruit. Pre-climacteric fruit were treated with 1-MCP vapors at a concentration of 500 parts per billion (v/v) at 23°C. 1-MCP prevented the climacteric rise of ethylene production, respiration, and volatile production, while untreated fruits developed typical climacteric changes in ethylene production, respiration and volatile production. Applying ethylene at 15–20 parts per million for 24 hr 11 days after 1-MCP treatment could not overcome the effect of 1-MCP, suggesting that 1-MCP inhibited ethylene action irreversibly. Interestingly, when 1-MCP-treated tissue were fed butanol and butyric acid, they converted these compounds to their corresponding esters butylacetate and butylbutanoate. Thus precursor supply is apparently limiting and appears to be ethylene-dependent.

Download Full-text

Brassinosteroids Suppress Ethylene Biosynthesis via Transcription Factor BZR1 in Pear and Apple Fruit

10.1101/2020.02.27.968800 ◽

2020 ◽

Author(s):

Yinglin Ji ◽

Yi Qu ◽

Zhongyu Jiang ◽

Xin Su ◽

Pengtao Yue ◽

...

Keyword(s):

Transcription Factor ◽

Fruit Ripening ◽

Ethylene Production ◽

Plant Hormone ◽

Expression Profiles ◽

Acc Synthase ◽

Ethylene Biosynthesis ◽

Apple Fruit ◽

Pear Fruit ◽

Climacteric Fruit

ABSTRACTThe plant hormone ethylene is important for the ripening of climacteric fruit, such as pear (Pyrus ussuriensis), and the brassinosteroid (BR) class of phytohormones affects ethylene biosynthesis during ripening, although via an unknown molecular mechanism. Here, we observed that exogenous BR treatment suppressed ethylene production during pear fruit ripening, and that the expression of the transcription factor PuBZR1 was enhanced by epibrassinolide (EBR) treatment during pear fruit ripening. PuBZR1 was shown to interact with PuACO1, which converts 1-aminocyclopropane-1-carboxylic acid (ACC) to ethylene, and suppress its activity. We also observed that BR-activated PuBZR1 bound to the promoters of PuACO1 and of PuACS1a, which encodes ACC synthase, and directly suppressed their transcription. Moreover, PuBZR1 suppressed the expression of transcription factor PuERF2 by binding its promoter, and PuERF2 bound to the promoters of PuACO1 and PuACS1a. We concluded that PuBZR1 indirectly suppresses the transcription of PuACO1 and PuACS1a through its regulation of PuERF2. Ethylene production and the expression profiles of the corresponding apple (Malus domestica) homologs showed similar changes following EBR treatment. Together, these results suggest that BR-activated BZR1 suppresses ACO1 activity and the expression of ACO1 and ACS1a, thereby reducing ethylene production during pear and apple fruit ripening. This likely represents a conserved mechanism by which exogenous BR suppresses ethylene biosynthesis during climacteric fruit ripening.One-sentence summaryBR-activated BZR1 suppresses ACO1 activity and expression of ACO1 and ACS1a, which encode two ethylene biosynthesis enzymes, thereby reducing ethylene production during pear and apple fruit ripening.

Download Full-text

Genetic Dissection of Phosphorus Use Efficiency in a Maize Association Population under Two P Levels in the Field

International Journal of Molecular Sciences ◽

10.3390/ijms22179311 ◽

2021 ◽

Vol 22 (17) ◽

pp. 9311

Author(s):

Dongdong Li ◽

Haoying Wang ◽

Meng Wang ◽

Guoliang Li ◽

Zhe Chen ◽

...

Keyword(s):

Grain Yield ◽

Genome Wide Association Study ◽

Crop Yields ◽

Tolerance Index ◽

Genetic Dissection ◽

Phosphorus Use Efficiency ◽

P Deficiency ◽

A Genome ◽

Zea May ◽

Use Efficiency

Phosphorus (P) deficiency is an important challenge the world faces while having to increase crop yields. It is therefore necessary to select maize (Zea may L.) genotypes with high phosphorus use efficiency (PUE). Here, we extensively analyzed the biomass, grain yield, and PUE-related traits of 359 maize inbred lines grown under both low-P and normal-P conditions. A significant decrease in grain yield per plant and biomass, an increase in PUE under low-P condition, as well as significant correlations between the two treatments were observed. In a genome-wide association study, 49, 53, and 48 candidate genes were identified for eleven traits under low-P, normal-P conditions, and in low-P tolerance index (phenotype under low-P divided by phenotype under normal-P condition) datasets, respectively. Several gene ontology pathways were enriched for the genes identified under low-P condition. In addition, seven key genes related to phosphate transporter or stress response were molecularly characterized. Further analyses uncovered the favorable haplotype for several core genes, which is less prevalent in modern lines but often enriched in a specific subpopulation. Collectively, our research provides progress in the genetic dissection and molecular characterization of PUE in maize.

Download Full-text

Genomic Dissection of Anthracnose (Colletotrichum sublineolum) Resistance Response in Sorghum Differential Line SC112-14

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401121 ◽

2020 ◽

Vol 10 (4) ◽

pp. 1403-1412

Author(s):

Clara M. Cruet-Burgos ◽

Hugo E. Cuevas ◽

Louis K. Prom ◽

Joseph E. Knoll ◽

Lauren R. Stutts ◽

...

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Recombinant Inbred Lines ◽

Genome Scan ◽

The United States ◽

Resistance Locus ◽

Chromosome 5 ◽

Resistance Response ◽

Colletotrichum Sublineolum ◽

A Genome

Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum, is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.

Download Full-text