Association mapping of leaf traits, flowering time, and phytate content in Brassica rapa

Genome ◽  
2007 ◽  
Vol 50 (10) ◽  
pp. 963-973 ◽  
Author(s):  
Jianjun Zhao ◽  
Maria-João Paulo ◽  
Diaan Jamar ◽  
Ping Lou ◽  
Fred van Eeuwijk ◽  
...  
Keyword(s):  
Population Structure ◽  
Qtl Mapping ◽  
Association Mapping ◽  
Brassica Rapa ◽  
Morphological Traits ◽  
Genetic Basis ◽  
Leaf Traits ◽  
Structure Association ◽  
Phytate Content ◽  
Trait Associations

Association mapping was used to investigate the genetic basis of variation within Brassica rapa , which is an important vegetable and oil crop. We analyzed the variation of phytate and phosphate levels in seeds and leaves and additional developmental and morphological traits in a set of diverse B. rapa accessions and tested association of these traits with AFLP markers. The analysis of population structure revealed four subgroups in the population. Trait values differed between these subgroups, thus defining associations between population structure and trait values, even for traits such as phytate and phosphate levels. Marker–trait associations were investigated both with and without taking population structure into account. One hundred and seventy markers were found to be associated with the observed traits without correction for population structure. Association analysis with correction for population structure led to the identification of 27 markers, 6 of which had known map positions; 3 of these were confirmed in additional QTL mapping studies.

scholarly journals The direction of genital asymmetry is expressed stochastically in internally fertilizing anablepid fishes

2020 ◽  
Vol 287 (1930) ◽  
pp. 20200969
Author(s):  
Julián Torres-Dowdall ◽  
Sina J. Rometsch ◽  
Andreas F. Kautt ◽  
Gastón Aguilera ◽  
Axel Meyer
Keyword(s):  
Population Structure ◽  
Phenotypic Variation ◽  
Morphological Traits ◽  
Genetic Basis ◽  
Genetic Differences ◽  
Association Analyses ◽  
Genome Wide ◽  
Representative Species ◽  
Genome Wide Data ◽  
Left And Right

Animal genitalia vary considerably across taxa, with divergence in many morphological traits, including striking departures from symmetry. Different mechanisms have been proposed to explain this diversity, mostly assuming that at least some of the phenotypic variation is heritable. However, heritability of the direction of genital asymmetry has been rarely determined. Anablepidae are internally fertilizing fish where the anal fin of males has been modified into an intromittent organ that transfers sperm into the gonopore of females. Males of anablepid fishes exhibit asymmetric genitalia, and both left- and right-sided individuals are commonly found at similar proportions within populations (i.e. antisymmetry). Although this polymorphism was described over a century ago, there have been no attempts to determine if genital asymmetry has a genetic basis and whether the different morphs are accumulating genetic differences, as might be expected since in some species females have also asymmetric gonopores and thereby can only be fertilized by compatible asymmetric males. We address this issue by combining breeding experiments with genome-wide data (ddRAD markers) in representative species of the two anablepid genera with asymmetric genitalia: Anableps and Jenynsia . Breeding experiments showed that all offspring were asymmetric, but their morphotype (i.e. right- or left-sided) was independent of parental morphotype, implying that the direction of asymmetry does not have a strong genetic component. Consistent with this conclusion, association analyses based on approximately 25 000 SNPs did not identify markers significantly associated with the direction of genital asymmetry and there was no evidence of population structure between left- and right-sided individuals. These results suggest that the direction of genital asymmetry in anablepid fishes might be stochastic, a commonly observed pattern in species with antisymmetry in morphological traits.

Identification and validation of functional markers in a global rice collection by association mapping

Genome ◽  
2014 ◽  
Vol 57 (6) ◽  
pp. 355-362 ◽  
Author(s):  
Mojtaba Jahani ◽  
Ghorbanali Nematzadeh ◽  
Behnaz Dolatabadi ◽  
Sayyed Hamidreza Hashemi ◽  
Ghasem Mohammadi-Nejad
Keyword(s):  
Population Structure ◽  
Molecular Markers ◽  
Association Mapping ◽  
Marker Assisted Selection ◽  
Multiple Testing ◽  
Morphological Traits ◽  
Mixed Linear Model ◽  
Width Ratio ◽  
Functional Markers ◽  
Population Structure Analysis

Recent results indicate that marker-assisted selection is an effective approach to reduce the cost and to improve the efficacy and accuracy of selection in plant breeding. This study was conducted to identify and validate molecular markers linked to important breeding traits by association mapping. The association was evaluated between 81 molecular markers (STS, SSR, Indel, CAPS, and PCR-based SNP) and 15 morphological traits in a global panel of 100 rice (Oryza sativa) accessions. The population structure analysis identified three main subpopulations. Obvious kinship relationships were also detected between the rice accessions. Association analysis was performed based on the mixed linear model by considering population structure and family relatedness. In addition, the false discovery rate method was used to correct the multiple testing. A total of 47 marker–trait associations were identified, including 22 markers for 14 traits. Among all, the polymorphism at the loci DDR-GL was highly associated with grain characters (grain length, grain width, and length/width ratio). In addition, marker RM3148 was responsible for five important traits simultaneously. Results demonstrated that such informative markers can be very useful for rice breeding programs using marker-assisted selection. Moreover, the diverse populations of rice accessions are a valuable resource for association mapping of morphological traits.

Natural variations of BrHISN2 provide a genetic basis for growth‐flavour trade‐off in different Brassica rapa subspecies

2021 ◽  
Author(s):  
Tongbing Su ◽  
Weihong Wang ◽  
Peirong Li ◽  
Xiaoyun Xin ◽  
Yangjun Yu ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Genetic Basis ◽  
Trade Off ◽  
Natural Variations

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.

Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 884-898 ◽  
Author(s):  
Jianjun Zhao ◽  
Anna Artemyeva ◽  
Dunia Pino Del Carpio ◽  
Ram Kumar Basnet ◽  
Ningwen Zhang ◽  
...  
Keyword(s):  
Association Mapping ◽  
Flowering Time ◽  
Brassica Rapa ◽  
Core Collection ◽  
Field Experiments ◽  
Research Centre ◽  
Candidate Gene Approach ◽  
Core Collections ◽  
Genome Wide ◽  
Using Data

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

scholarly journals Analysis of the genetic basis of plant height-related traits in response to ethylene by QTL mapping in maize (Zea mays L.)

PLoS ONE ◽  
2018 ◽  
Vol 13 (2) ◽  
pp. e0193072
Author(s):  
Weiqiang Zhang ◽  
Zhi Li ◽  
Hui Fang ◽  
Mingcai Zhang ◽  
Liusheng Duan
Keyword(s):  
Zea Mays ◽  
Qtl Mapping ◽  
Plant Height ◽  
Genetic Basis ◽  
Zea Mays L

scholarly journals A Genomic Variation Map Provides Insights into the Genetic Basis of Spring Chinese Cabbage (Brassica rapa ssp. pekinensis) Selection

2018 ◽  
Vol 11 (11) ◽  
pp. 1360-1376 ◽  
Author(s):  
Tongbing Su ◽  
Weihong Wang ◽  
Peirong Li ◽  
Bin Zhang ◽  
Pan Li ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Genetic Basis ◽  
Genomic Variation
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