Novel candidate genes influencing natural variation in potato tuber cold sweetening identified by comparative proteomics and association mapping

Heat and drought, individually or in combination, limit pea productivity. Fortunately, substantial genetic diversity exists in pea germplasm for traits related to abiotic stress resistance. Understanding the genetic basis of resistance could accelerate the development of stress-adaptive cultivars. We conducted a genome-wide association study (GWAS) in pea on six stress-adaptive traits with the aim to detect the genetic regions controlling these traits. One hundred and thirty-five genetically diverse pea accessions were phenotyped in field studies across three or five environments under stress and control conditions. To determine marker trait associations (MTAs), a total of 16,877 valuable single nucleotide polymorphisms (SNPs) were used in association analysis. Association mapping detected 15 MTAs that were significantly (p ≤ 0.0005) associated with the six stress-adaptive traits averaged across all environments and consistent in multiple individual environments. The identified MTAs were four for lamina wax, three for petiole wax, three for stem thickness, two for the flowering duration, one for the normalized difference vegetation index (NDVI), and two for the normalized pigment and chlorophyll index (NPCI). Sixteen candidate genes were identified within a 15 kb distance from either side of the markers. The detected MTAs and candidate genes have prospective use towards selecting stress-hardy pea cultivars in marker-assisted selection.

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A combined association mapping and t-test analysis of SNP loci and candidate genes involving in resistance to low nitrogen traits by a wheat mutant population

PLoS ONE ◽

10.1371/journal.pone.0211492 ◽

2019 ◽

Vol 14 (1) ◽

pp. e0211492 ◽

Cited By ~ 5

Author(s):

Hongchun Xiong ◽

Huijun Guo ◽

Chunyun Zhou ◽

Xiaotong Guo ◽

Yongdun Xie ◽

...

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

T Test ◽

Test Analysis ◽

Mutant Population ◽

Low Nitrogen ◽

Wheat Mutant

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Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage

BMC Plant Biology ◽

10.1186/s12870-019-1828-5 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 10

Author(s):

Adel H. Abdel-Ghani ◽

Rajiv Sharma ◽

Celestine Wabila ◽

Sidram Dhanagond ◽

Saed J. Owais ◽

...

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Spring Barley ◽

Seedling Stage ◽

Genome Wide Association ◽

Genome Wide ◽

Shoot Architecture

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Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat

International Journal of Molecular Sciences ◽

10.3390/ijms21020394 ◽

2020 ◽

Vol 21 (2) ◽

pp. 394 ◽

Cited By ~ 2

Author(s):

Daniela Marone ◽

Monica Rodriguez ◽

Sergio Saia ◽

Roberto Papa ◽

Domenico Rau ◽

...

Keyword(s):

Plant Growth ◽

Association Mapping ◽

Durum Wheat ◽

Candidate Genes ◽

Zinc Finger ◽

Growth Habit ◽

Genome Wide Association ◽

Genome Wide ◽

Plant Growth Habit ◽

Tiller Angle

By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.

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Genetic Networks Underlying Natural Variation in Basal and Induced Activity Levels in Drosophila melanogaster

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.401034 ◽

2020 ◽

Vol 10 (4) ◽

pp. 1247-1260 ◽

Cited By ~ 4

Author(s):

Louis P. Watanabe ◽

Cameron Gordon ◽

Mina Y. Momeni ◽

Nicole C. Riddle

Keyword(s):

Drosophila Melanogaster ◽

Candidate Genes ◽

Genetic Architecture ◽

Natural Variation ◽

Neuromuscular Junctions ◽

Healthy Lifestyle ◽

Activity Levels ◽

Exercise Activity ◽

The Central Nervous System ◽

Exercise Induced

Exercise is recommended by health professionals across the globe as part of a healthy lifestyle to prevent and/or treat the consequences of obesity. While overall, the health benefits of exercise and an active lifestyle are well understood, very little is known about how genetics impacts an individual’s inclination for and response to exercise. To address this knowledge gap, we investigated the genetic architecture underlying natural variation in activity levels in the model system Drosophila melanogaster. Activity levels were assayed in the Drosophila Genetics Reference Panel fly strains at baseline and in response to a gentle exercise treatment using the Rotational Exercise Quantification System. We found significant, sex-dependent variation in both activity measures and identified over 100 genes that contribute to basal and induced exercise activity levels. This gene set was enriched for genes with functions in the central nervous system and in neuromuscular junctions and included several candidate genes with known activity phenotypes such as flightlessness or uncoordinated movement. Interestingly, there were also several chromatin proteins among the candidate genes, two of which were validated and shown to impact activity levels. Thus, the study described here reveals the complex genetic architecture controlling basal and exercise-induced activity levels in D. melanogaster and provides a resource for exercise biologists.

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