Accelerating the Development of Heat Tolerant Tomato Hybrids through a Multi-Traits Evaluation of Parental Lines Combining Phenotypic and Genotypic Analysis

The constitution of heat tolerant F1 hybrids is a challenge to ensure high yield and good fruit quality in the global climate. In the present work, we evaluated 15 genotypes for yield-related traits highly affected by high temperatures (HT). This phenotypic analysis allowed to identify four parental genotypes showing promising yield performances under HT conditions. Two of these genotypes also exhibited good fruit quality traits. A molecular marker analysis was carried out for six resistance genes to pathogens mostly affecting tomatoes. This analysis evidenced the presence of a maximum of three resistant alleles in parental genotypes. Exploring single nucleotide polymorphisms (SNPs) revealed by two high-throughput genotyping platforms allowed identifying additional 12 genes potentially involved in resistance to biotic stress, to be further investigated. Following these considerations, 13 F1 hybrids were constituted combining the parental genotypes and then evaluated for multiple traits under HT conditions. By estimating a hybrid index based on yield performances, desirable quality and resistance gene, we identified seven hybrids showing the best performances. The promising results obtained in the present work should be confirmed by evaluating the best hybrids selected for additional years and environments before proposing them as novel commercial hybrids that could maintain high performances under HT conditions.

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L2,1-norm regularized multivariate regression model with applications to genomic prediction

Bioinformatics ◽

10.1093/bioinformatics/btab212 ◽

2021 ◽

Author(s):

Alain J Mbebi ◽

Hao Tong ◽

Zoran Nikoloski

Keyword(s):

Variable Selection ◽

Regression Model ◽

Multivariate Regression ◽

Statistical Testing ◽

Supplementary Information ◽

Nucleotide Polymorphisms ◽

Multiple Traits ◽

Multivariate Regression Model ◽

Proposed Model ◽

Iterative Optimization Algorithm

AbstractMotivationGenomic selection (GS) is currently deemed the most effective approach to speed up breeding of agricultural varieties. It has been recognized that consideration of multiple traits in GS can improve accuracy of prediction for traits of low heritability. However, since GS forgoes statistical testing with the idea of improving predictions, it does not facilitate mechanistic understanding of the contribution of particular single nucleotide polymorphisms (SNP).ResultsHere, we propose a L2,1-norm regularized multivariate regression model and devise a fast and efficient iterative optimization algorithm, called L2,1-joint, applicable in multi-trait GS. The usage of the L2,1-norm facilitates variable selection in a penalized multivariate regression that considers the relation between individuals, when the number of SNPs is much larger than the number of individuals. The capacity for variable selection allows us to define master regulators that can be used in a multi-trait GS setting to dissect the genetic architecture of the analyzed traits. Our comparative analyses demonstrate that the proposed model is a favorable candidate compared to existing state-of-the-art approaches. Prediction and variable selection with datasets from Brassica napus, wheat and Arabidopsis thaliana diversity panels are conducted to further showcase the performance of the proposed model.Availability and implementation: The model is implemented using R programming language and the code is freely available from https://github.com/alainmbebi/L21-norm-GS.Supplementary informationSupplementary data are available at Bioinformatics online.

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Genetic basis of phenotypic plasticity and genotype x environment interaction in a multi-parental population

10.1101/2020.02.07.938456 ◽

2020 ◽

Author(s):

Isidore Diouf ◽

Laurent Derivot ◽

Shai Koussevitzky ◽

Yolande Carretero ◽

Frédérique Bitton ◽

...

Keyword(s):

Phenotypic Plasticity ◽

Genetic Architecture ◽

Genetic Basis ◽

Linear Models ◽

Global Climate ◽

Functional Characterization ◽

Genotype X Environment Interaction ◽

Environment Interaction ◽

Multiple Traits ◽

Genotype X Environment

AbstractDeciphering the genetic basis of phenotypic plasticity and genotype x environment interaction (GxE) is of primary importance for plant breeding in the context of global climate change. Tomato is a widely cultivated crop that can grow in different geographical habitats and which evinces a great capacity of expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore GxE and plasticity for multiple traits measured in a multi-environment trial (MET) design comprising optimal cultural conditions and water deficit, salinity and heat stress over 12 environments. Substantial GxE was observed for all the traits measured. Different plasticity parameters were estimated through the Finlay-Wilkinson and factorial regression models and used together with the genotypic means for quantitative trait loci (QTL) mapping analyses. Mixed linear models were further used to investigate the presence of interactive QTLs (QEI). The results highlighted a complex genetic architecture of tomato plasticity and GxE. Candidate genes that might be involved in the occurrence of GxE were proposed, paving the way for functional characterization of stress response genes in tomato and breeding for climate-adapted crop.HighlightThe genetic architecture of tomato response to several abiotic stresses is deciphered. QTL for plasticity and QTL x Environment were identified in a highly recombinant MAGIC population.

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Development of sweet pepper F1 hybrids based on MAS methods by fruit quality and resistance genes

10.18699/plantgen2019-016 ◽

2019 ◽

Keyword(s):

Fruit Quality ◽

Resistance Genes ◽

Sweet Pepper ◽

F1 Hybrids

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Genome Size: A Novel Predictor of Nut Weight and Nut Size of Walnut Trees

HortScience ◽

10.21273/hortsci12725-17 ◽

2018 ◽

Vol 53 (3) ◽

pp. 275-282 ◽

Cited By ~ 5

Author(s):

Saadat Sarikhani Khorami ◽

Kazem Arzani ◽

Ghasem Karimzadeh ◽

Abdolali Shojaeiyan ◽

Wilco Ligterink

Keyword(s):

Genetic Diversity ◽

Genome Size ◽

Plant Genetic Resources ◽

Kernel Weight ◽

High Yield ◽

Phenotypic Analysis ◽

High Genetic Diversity ◽

Breeding Programs ◽

Superior Genotypes ◽

Southwest Of Iran

Plant genetic diversity is the fundamental of plant-breeding programs to improve desirable characteristics. Hence, evaluation of genetic diversity is the first step in fruit-breeding programs. Accordingly, the current study was carried out to evaluate 25 superior walnut genotypes in respect of phenotypic and cytological characteristics. For this purpose, 560 walnut genotypes in southwest of Iran were evaluated based on UPOV and International Plant Genetic Resources Institute (IPGRI) descriptor. After a 2-year primary evaluation, 25 superior genotypes were selected for future phenotypic and genome size assessment. Flow cytometry was used to estimate genome size of the selected superior genotypes. A high genetic diversity was found in walnut population collected from the southwest of Iran. The selected superior genotypes had high yield, lateral bearing, thin-shell thickness (0.90–1.64 mm), high nut (12.54–19.80 g) and kernel (7.02–9.91 g) weight with light (L) to extra light (EL) kernel color which easily can be removed from the shell. Also, FaBaCh2 genotype turned out to be protogynous being important as a pollinizer cultivar. In addition to extensive phenotypic analysis, genome size was determined. The studied genotypes were diploid (2n = 2x = 32) and varied in genome size from 1.29 (FaBaAv2) to 1.40 pg (FaBaNs12). Correlation analysis showed that lateral bearing, budbreak date, nut size, and weight were the main variables contributing to walnut production. A linear relationship was found between genome size and nut weight (r = 0.527**), kernel weight (r = 0.551**), and nut size index (NSI) (r = 0.487**). Therefore, genome size can be considered as a strong and valuable tool to predict nut and kernel weight and nut size.

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Genetic Basis of Maize Resistance to Multiple Insect Pests: Integrated Genome-Wide Comparative Mapping and Candidate Gene Prioritization

Genes ◽

10.3390/genes11060689 ◽

2020 ◽

Vol 11 (6) ◽

pp. 689

Author(s):

A. Badji ◽

D. B. Kwemoi ◽

L. Machida ◽

D. Okii ◽

N. Mwila ◽

...

Keyword(s):

Insect Resistance ◽

Defense Mechanisms ◽

Genome Wide Association Study ◽

Insect Pests ◽

Physical Map ◽

Fall Armyworm ◽

Nucleotide Polymorphisms ◽

Multiple Traits ◽

Maize Weevil ◽

Genome Wide

Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance to fall armyworm (FAW), whilst bulked grains were subjected to a maize weevil (MW) bioassay and genotyped with Diversity Array Technology’s single nucleotide polymorphisms (SNPs) markers. A multi-locus genome-wide association study (GWAS) revealed 62 quantitative trait nucleotides (QTNs) associated with FAW and MW resistance traits on all 10 maize chromosomes, of which, 47 and 31 were discovered at stringent Bonferroni genome-wide significance levels of 0.05 and 0.01, respectively, and located within or close to multiple insect resistance genomic regions (MIRGRs) concerning FAW, SB, and MW. Sixteen QTNs influenced multiple traits, of which, six were associated with resistance to both FAW and MW, suggesting a pleiotropic genetic control. Functional prioritization of candidate genes (CGs) located within 10–30 kb of the QTNs revealed 64 putative GWAS-based CGs (GbCGs) showing evidence of involvement in plant defense mechanisms. Only one GbCG was associated with each of the five of the six combined resistance QTNs, thus reinforcing the pleiotropy hypothesis. In addition, through in silico co-functional network inferences, an additional 107 network-based CGs (NbCGs), biologically connected to the 64 GbCGs, and differentially expressed under biotic or abiotic stress, were revealed within MIRGRs. The provided multiple insect resistance physical map should contribute to the development of combined insect resistance in maize.

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ABO GENE AND AGING-RELATED OUTCOMES IN OVER 379,000 EUROPEAN-DESCENT PARTICIPANTS OF UK BIOBANK

Innovation in Aging ◽

10.1093/geroni/igz038.3369 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

pp. S925-S925

Author(s):

Chia-Ling Kuo ◽

Ziwei Pan ◽

Luke C Pilling ◽

George A Kuchel ◽

David Melzer

Keyword(s):

Breast Cancer ◽

Type Ii Diabetes ◽

Hemoglobin Concentration ◽

Blood Type ◽

Type Ii ◽

Nucleotide Polymorphisms ◽

Multiple Traits ◽

Mineral Density ◽

Blood Types ◽

Wide Range

Abstract Genetic variants associated with multiple traits are potential targets to delay aging. Drugs supported by genetic evidence are twice as likely to succeed in human trials. Single nucleotide polymorphisms (SNPs) in the ABO gene were reported by genome-wide associations studies, associated with breast cancer, coronary artery disease, stroke, and type II diabetes. To evaluate the potential of ABO gene as a target for aging intervention, we conducted a phenome-wide association study (PheWAS) to associate the genotype-derived blood types (based on two SNPs in the ABO gene) with a wide range of aging-related outcomes. The genotype-derived blood type distribution (41% A, 9% B, 3% AB, and 47% O) is similar to that reported by the UK National Health Service (39% A, 10% B, 3% AB, and 48% O). The blood type was not associated with parental lifespan or extreme parental longevity. Non-O types had modestly lower risk of hypertension than O type but higher risk of type II diabetes and pancreatic cancer (e.g., OR= 1.37, 95% CI: 1.17 to 1.59 comparing A to O). Additionally, “A" type had modestly higher risk of breast cancer than other types. “A” allele (in A or AB type) was associated with lower heel bone mineral density, alkaline phosphatase (e.g., 0.41 standard deviation lower in A than that in O, 95% CI: -0.42 to -0.40), and hemoglobin concentration, but higher HbA1c, direct LDL, and cholesterol. Blood types with A allele(s) are less favored than other blood types, which however are adversely associated with some aging traits.

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Combining phenotype, genotype and environment to uncover genetic components underlying water use efficiency in Persian walnut

Journal of Experimental Botany ◽

10.1093/jxb/erz467 ◽

2019 ◽

Author(s):

Mohammad Mehdi Arab ◽

Annarita Marrano ◽

Rostam Abdollahi-Arpanahi ◽

Charles A Leslie ◽

Hao Cheng ◽

...

Keyword(s):

Water Use Efficiency ◽

Water Use ◽

Leaf Growth ◽

Stress Index ◽

Phenotypic Traits ◽

Nucleotide Polymorphisms ◽

Multiple Traits ◽

Persian Walnut ◽

Genetic Components ◽

Use Efficiency

Abstract Walnut production is challenged by climate change and abiotic stresses. Elucidating the genomic basis of adaptation to climate is essential to breeding drought tolerant cultivars for enhanced productivity in arid and semi-arid regions. Here, we aimed to identify loci potentially involved in water use efficiency (WUE) and adaptation to drought in Persian walnut using a diverse panel of 95 walnut families (950 seedlings) from Iran, which show contrasting levels of water availability in their native habitats. We analyzed associations between phenotypic, genotypic, and environmental variables from datasets of 609 K high-quality single-nucleotide polymorphisms (SNPs), three categories of phenotypic traits (WUE related traits under drought, their drought stress index and principal components), and 21 climate variables and combination of them (first three PCs). Our genotype-phenotype analysis identified 22 significant and 266 suggestive associations, some of which were identified for multiple traits, suggesting their correlation and a possible common genetic control. Also, genotype-environment association analysis found 115 significant and 265 suggestive SNP loci that displayed potential signals of local adaptation. Several sets of stress-responsive genes were found in the genomic regions significantly associated with the aforementioned traits. Most of the candidate genes identified are involved in abscisic acid signaling, stomatal regulation, transduction of environmental signals, antioxidant defense system, osmotic adjustment, and leaf growth and development. Upon validation, the marker-trait associations identified for drought tolerance-related traits would allow the selection and development of new walnut rootstocks or scion cultivars with superior water use efficiency.

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Whole-Genome Sequencing and Phenotypic Analysis of Bacillus subtilis Mutants following Evolution under Conditions of Relaxed Selection for Sporulation

Applied and Environmental Microbiology ◽

10.1128/aem.05272-11 ◽

2011 ◽

Vol 77 (19) ◽

pp. 6867-6877 ◽

Cited By ~ 20

Author(s):

Christopher T. Brown ◽

Laura K. Fishwick ◽

Binna M. Chokshi ◽

Marissa A. Cuff ◽

Jay M. Jackson ◽

...

Keyword(s):

Bacillus Subtilis ◽

Chromosomal Rearrangements ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Relaxed Selection ◽

Phenotypic Analysis ◽

Competitive Fitness ◽

Content Type ◽

Intergenic Regions ◽

Selection For

ABSTRACTLittle is known about how genetic variation at the nucleotide level contributes to competitive fitness within species. During a 6,000-generation study ofBacillus subtilisevolved under relaxed selection for sporulation, a new strain, designated WN716, emerged with significantly different colony and cell morphologies; loss of sporulation, competence, acetoin production, and motility; multiple auxotrophies; and increased competitive fitness (H. Maughan and W. L. Nicholson, Appl. Environ. Microbiol.77:4105–4118, 2011). The genome of WN716 was analyzed by OpGen optical mapping, whole-genome 454 pyrosequencing, and the CLC Genomics Workbench. No large chromosomal rearrangements were found; however, 34 single-nucleotide polymorphisms (SNPs) and +1 frameshifts were identified in WN716 that resulted in amino acid changes in coding sequences of annotated genes, and 11 SNPs were located in intergenic regions. Several classes of genes were affected, including biosynthetic pathways, sporulation, competence, and DNA repair. In several cases, attempts were made to link observed phenotypes of WN716 with the discovered mutations, with various degrees of success. For example, a +1 frameshift was identified at codon 13 ofsigW, the product of which (SigW) controls a regulon of genes involved in resistance to bacteriocins and membrane-damaging antibiotics. Consistent with this finding, WN716 exhibited sensitivity to fosfomycin and to a bacteriocin produced byB. subtilissubsp.spizizeniiand exhibited downregulation of SigW-dependent genes on a transcriptional microarray, consistent with WN716 carrying a knockout ofsigW. The results suggest that propagation ofB. subtilisfor less than 2,000 generations in a nutrient-rich environment where sporulation is suppressed led to rapid initiation of genomic erosion.

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QTL analysis of yield-related traits and their association with functional markers in Brassica napus L.

Australian Journal of Agricultural Research ◽

10.1071/ar06350 ◽

2007 ◽

Vol 58 (8) ◽

pp. 759 ◽

Cited By ~ 26

Author(s):

Yuanyuan Li ◽

Jinxiong Shen ◽

Tonghua Wang ◽

Qingfang Chen ◽

Xingguo Zhang ◽

...

Keyword(s):

Brassica Napus ◽

Agronomic Traits ◽

High Yield ◽

Functional Markers ◽

Multiple Traits ◽

Brassica Napus L ◽

Breeding Programs ◽

F2 Population ◽

Expressed Sequence ◽

Simple Sequence

Yield is one of the most important traits in Brassica napus breeding programs. Quantitative trait loci (QTLs) for yield-related traits based on genetic mapping would help breeders to develop high-yield cultivars. In this study, a genetic linkage map of B. napus, containing 142 sequence-related amplified polymorphism (SRAP) markers, 163 functional markers, 160 simple sequence repeat (SSR) markers, and 117 amplified fragment length polymorphism (AFLP) markers, was constructed in an F2 population of 184 individuals resulting from the cross SI-1300 × Eagle. This map covered 2054.51 cM with an average marker interval of 3.53 cM. Subsequently, QTLs were detected for 12 yield-related traits in Wuhan and Jingmen. In total, 133 QTLs were identified, including 14 consistent ones across the 2 locations. Fifteen of 20 linkage groups (LGs) were found to have QTLs for the 12 traits investigated, and most of the QTLs were clustered, especially on LGs N2 and N7, where similar QTL positions were identified for multiple traits. Eight of 10 QTLs for yield per plant (YP) were also associated with number of seeds per silique (SS), number of siliques per plant (SP), and/or 1000-seed weight (SW). In addition, 45 functional markers involved in 39 expressed sequence tags (ESTs) were linked to the QTLs of 12 traits. The present results may serve as a valuable basis for further molecular dissection of agronomic traits in B. napus, and the markers related to QTLs may offer promising possible makers for marker assisted selection.

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Genetic Basis of Maize Resistance to Multiple-Insect Pests: Integrated Genome-Wide Comparative Mapping and Candidate Gene Prioritization

10.20944/preprints202005.0337.v1 ◽

2020 ◽

Author(s):

Arfang BADJI ◽

Daniel Bomet KWEMOI ◽

Lewis MACHIDA ◽

Dennis OKII ◽

Natasha MWILA ◽

...

Keyword(s):

Insect Resistance ◽

Defense Mechanisms ◽

Genome Wide Association Study ◽

Insect Pests ◽

Physical Map ◽

Nucleotide Polymorphisms ◽

Multiple Traits ◽

Significance Level ◽

Mapping Panel ◽

Genome Wide

Several herbivores feed on maize in field and storage setups making the development of multiple-insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance to FAW whilst bulked grains were subjected to MW bioassay, genotyped with Diversity Array Technologies single nucleotide polymorphisms (SNPs) markers. A multi-locus genome-wide association study (GWAS) revealed 62 quantitative trait nucleotides (QTNs) associated with FAW and MW resistance traits on all 10 maize chromosomes, of which, 47 and 31 were discovered at stringent Bonferroni genome-wide significance level of 0.05 and 0.01, respectively, and located within or close to multiple-insect resistance genomic regions (MIRGRs) concerning FAW, SB, and MW. Sixteen QTNs influenced multiple-traits of which six were associated with resistance to both FAW and MW suggesting a pleiotropic genetic control. Functional prioritization of candidate genes (CGs) located within 10-30kb of the QTNs revealed 64 putative GWAS-based CGs (GbCGs) showing evidence of involvement in plant defense mechanisms. Only one GbCG was associated with each of five of the six combined-resistance QTNs, thus, reinforcing the pleiotropy hypothesis. In addition, through In-silico co-functional network inferences, an additional 107 Network-based CGs (NbCGs), biologically connected to the 64 GbCGs, differentially expressed under biotic or abiotic stress were revealed within MIRGRs. The provided multiple-insect resistance physical map should contribute to the development of combined-insect resistance in maize.

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