scholarly journals Genome-Wide Transcriptome Analysis of Two Contrasting Brassica rapa Doubled Haploid Lines under Cold-Stresses Using Br135K Oligomeric Chip

PLoS ONE ◽  
2014 ◽  
Vol 9 (8) ◽  
pp. e106069 ◽  
Author(s):  
Hee-Jeong Jung ◽  
Xiangshu Dong ◽  
Jong-In Park ◽  
Senthil Kumar Thamilarasan ◽  
Sang Sook Lee ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Doubled Haploid ◽  
Transcriptome Analysis ◽  
Doubled Haploid Lines ◽  
Genome Wide

scholarly journals QTL Analysis of the Content of Some Bioactive Compounds in Brassica rapa L. Grown under Light Culture Conditions

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 583
Author(s):  
Ksenia V. Egorova ◽  
Nadezhda G. Sinyavina ◽  
Anna M. Artemyeva ◽  
Natalia V. Kocherina ◽  
Yuriy V. Chesnokov
Keyword(s):  
Molecular Markers ◽  
Brassica Rapa ◽  
Doubled Haploid ◽  
Biochemical Composition ◽  
Dry Matter ◽  
Culture Conditions ◽  
Biologically Active Compounds ◽  
Biologically Active ◽  
Active Compounds ◽  
Doubled Haploid Lines

The article presents the results of biochemical and QTL (Quantitative Trait Loci) analysis of dry matter content, nutrient and biologically active compounds: sugars, ascorbic acid, chlorophylls a and b, anthocyanins and carotenoids in populations of doubled haploid lines of leaf, root crops, and oilseeds of the Brassica rapa L. species grown in optimal light culture conditions, but with different photoperiod durations. The purpose of this study was to evaluate the effect of the photoperiod on the transition to bolting and the accumulation of biologically active substances, as well as how the localization and identification of chromosomal loci determined the content of certain phytochemicals. The influence of the length of daylight hours on the content of components of the biochemical composition was assessed. It was shown that growing under conditions of a 16 h photoperiod increased the content of dry matter, sugars, vitamin C, and anthocyanins. On the contrary, the content of photosynthetic pigments was higher under the conditions of a 12 h photoperiod. Valuable lines that can be sources of biologically active compounds were revealed. Based on the results of the obtained data, 102 QTLs were mapped, which determine the manifestation of the studied biochemical quality traits in the B. rapa doubled haploid lines under conditions of short and long daylight hours. Molecular markers genetically linked to the selected QTLs were determined. It was revealed that the identified loci controlling all the studied biochemical traits were mainly in the fifth, sixth, seventh, and ninth linkage groups, which correlated with the data obtained in the field and greenhouse. Most of the identified loci controlled several studied traits simultaneously. The identified QTLs and identified molecular markers are of interest for further study of the genetic control of the economically valuable traits determined by them and for the implementation of marker-assisted selection in B. rapa. The data obtained can be used in genetic and breeding work, including for the obtaining of new genotypes, lines and cultivars with a valuable biochemical composition, adapted for cultivation under specific photoperiodic conditions.

Genome-Wide Association and Transcriptome Analysis Reveals Total Serum Ghrelin to Be Linked with GFRAL

2020 ◽  
Author(s):  
Dirk Alexander Wittekind ◽  
Markus Scholz ◽  
Jürgen Kratzsch ◽  
Markus Loeffler ◽  
Katrin Horn ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Genome Wide Association ◽  
Total Serum ◽  
Genome Wide ◽  
Serum Ghrelin

scholarly journals Identification, Expression and Evolution of Short-Chain Dehydrogenases/Reductases in Nile Tilapia (Oreochromis niloticus)

2021 ◽  
Vol 22 (8) ◽  
pp. 4201
Author(s):  
Shuai Zhang ◽  
Lang Xie ◽  
Shuqing Zheng ◽  
Baoyue Lu ◽  
Wenjing Tao ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Tandem Duplication ◽  
Developmental Stages ◽  
Short Chain ◽  
Sexually Dimorphic ◽  
Physiological Processes ◽  
Genome Wide ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Tandem Duplications

The short-chain dehydrogenases/reductases (SDR) superfamily is involved in multiple physiological processes. In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases. Overall, the number of SDR genes in animals increased with whole genome duplication (WGD), suggesting the expansion of SDRs during evolution, especially in 3R-WGD and polyploidization of teleosts. Phylogenetic analysis indicated that vertebrates SDRs were clustered into five categories: classical, extended, undefined, atypical, and complex. Moreover, tandem duplication of hpgd-a, rdh8b and dhrs13 was observed in teleosts analyzed. Additionally, tandem duplications of dhrs11-a, dhrs7a, hsd11b1b, and cbr1-a were observed in all cichlids analyzed, and tandem duplication of rdh10-b was observed in tilapiines. Transcriptome analysis of adult fish revealed that 93 SDRs were expressed in more than one tissue and 5 in one tissue only. Transcriptome analysis of gonads from different developmental stages showed that expression of 17 SDRs were sexually dimorphic with 11 higher in ovary and 6 higher in testis. The sexually dimorphic expressions of these SDRs were confirmed by in situ hybridization (ISH) and qPCR, indicating their possible roles in steroidogenesis and gonadal differentiation. Taken together, the identification and the expression data obtained in this study contribute to a better understanding of SDR superfamily evolution and functions in teleosts.

scholarly journals Genome-wide transcriptome analysis of microspore abortion initiation in radish (Raphanus sativus L.)

Gene ◽  
2021 ◽  
pp. 145753
Author(s):  
Chen Liu ◽  
Weimin Fu ◽  
Wenling Xu ◽  
Xianxian Liu ◽  
Shufen Wang
Keyword(s):  
Transcriptome Analysis ◽  
Raphanus Sativus ◽  
Genome Wide ◽  
Raphanus Sativus L

Genome-wide identification and abiotic stress-responsive expression of MLP family genes in Brassica rapa

Gene Reports ◽  
2020 ◽  
Vol 21 ◽  
pp. 100919
Author(s):  
Jiaxin Zeng ◽  
Yuxuan Ruan ◽  
Boyu Liu ◽  
Ying Ruan ◽  
Yong Huang
Keyword(s):  
Abiotic Stress ◽  
Brassica Rapa ◽  
Genome Wide

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.

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