Genome-wide identification of ABA receptor PYL/RCAR gene family and their response to cold stress in Medicago sativa L

Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger’s positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.

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Genome-Wide Identification and Expression Analysis of the SRS Gene Family in Medicago sativa

DNA and Cell Biology ◽

10.1089/dna.2021.0462 ◽

2021 ◽

Vol 40 (12) ◽

pp. 1539-1553

Author(s):

Yingbo Yang ◽

Lin Qi ◽

Lili Nian ◽

Xiaolin Zhu ◽

Xianfeng Yi ◽

...

Keyword(s):

Gene Family ◽

Medicago Sativa ◽

Expression Analysis ◽

Genome Wide

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Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽

10.3390/genes12121867 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1867

Author(s):

Yan Li ◽

Xiang Li ◽

Jiatong Wei ◽

Kewei Cai ◽

Hongzhi Zhang ◽

...

Keyword(s):

Transcription Factors ◽

Stress Response ◽

Cold Stress ◽

Gene Family ◽

Gene Families ◽

Regulatory Function ◽

Wrky Gene ◽

Wrky Transcription Factors ◽

Biotic Stresses ◽

Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

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Strategies to Increase Prediction Accuracy in Genomic Selection of Complex Traits in Alfalfa (Medicago sativa L.)

Cells ◽

10.3390/cells10123372 ◽

2021 ◽

Vol 10 (12) ◽

pp. 3372

Author(s):

Cesar A. Medina ◽

Harpreet Kaur ◽

Ian Ray ◽

Long-Xi Yu

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Medicago Sativa ◽

Genomic Selection ◽

Complex Traits ◽

Prediction Accuracy ◽

Breeding Value ◽

Phenotypic Traits ◽

Genome Wide ◽

Medicago Sativa L

Agronomic traits such as biomass yield and abiotic stress tolerance are genetically complex and challenging to improve through conventional breeding approaches. Genomic selection (GS) is an alternative approach in which genome-wide markers are used to determine the genomic estimated breeding value (GEBV) of individuals in a population. In alfalfa (Medicago sativa L.), previous results indicated that low to moderate prediction accuracy values (<70%) were obtained in complex traits, such as yield and abiotic stress resistance. There is a need to increase the prediction value in order to employ GS in breeding programs. In this paper we reviewed different statistic models and their applications in polyploid crops, such as alfalfa and potato. Specifically, we used empirical data affiliated with alfalfa yield under salt stress to investigate approaches that use DNA marker importance values derived from machine learning models, and genome-wide association studies (GWAS) of marker-trait association scores based on different GWASpoly models, in weighted GBLUP analyses. This approach increased prediction accuracies from 50% to more than 80% for alfalfa yield under salt stress. Finally, we expended the weighted GBLUP approach to potato and analyzed 13 phenotypic traits and obtained similar results. This is the first report on alfalfa to use variable importance and GWAS-assisted approaches to increase the prediction accuracy of GS, thus helping to select superior alfalfa lines based on their GEBVs.

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The Affymetrix Medicago GeneChip® array is applicable for transcript analysis of alfalfa (Medicago sativa)

Functional Plant Biology ◽

10.1071/fp06065 ◽

2006 ◽

Vol 33 (8) ◽

pp. 783 ◽

Cited By ~ 23

Author(s):

Mesfin Tesfaye ◽

Kevin A. T. Silverstein ◽

Bruna Bucciarelli ◽

Deborah A. Samac ◽

Carroll P. Vance

Keyword(s):

Medicago Sativa ◽

Transcript Analysis ◽

Crop Species ◽

Trifoliate Leaf ◽

Model Legume ◽

Genome Wide ◽

Medicago Sativa L ◽

Genome Array ◽

Medicago Species ◽

Medicago Genechip

The recently released Affymetrix GeneChip® Medicago Genome Array contains approximately 52 700 probe sets representing genes in both the model legume Medicago truncatula Gaertn. and the closely related crop species Medicago sativa L. (alfalfa). We evaluated the utility of the Medicago GeneChip® for monitoring genome-wide expression of M. truncatula and alfalfa seedlings grown to the first trifoliate leaf stage. We found that approximately 40–54% of the Medicago probes were detected in leaf or root samples of alfalfa or M. truncatula. Approximately 45–59% of the detected Medicago probes were called ‘present’ in all replicate GeneChips of Medicago species, indicating a considerable overlap in the number and type of Medicago probes detected between root and leaf organs. Nevertheless, gene expression differences between roots and leaf organs accounted for approximately 17% of the total variation, regardless of the Medicago species from which the samples were harvested. The result shows that the Medicago GeneChip® is applicable for transcript analysis for both alfalfa and M. truncatula.

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