Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.)

Lectin receptor-like kinases (LecRLKs) are involved in responses to diverse environmental stresses and pathogenic microbes. A comprehensive acknowledgment of the family members in potato (Solanum tuberosum) genome is largely limited until now. In total, 113 potato LecRLKs (StLecRLKs) were first identified, including 85 G-type, 26 L-type and 2 C-type members. Based on phylogenetic analysis, StLecRLKs were sub-grouped into seven clades, including C-type, L-type, G-I, G-II, G-III G-IV and G-V. Chromosomal distribution and gene duplication analysis revealed the expansion of StLecRLKs occurred majorly through tandem duplication although the whole-genome duplication (WGD)/segmental duplication events were found. Cis-elements in the StLecRLKs promoter region responded mainly to signals of defense and stress, phytohormone, biotic or abiotic stress. Moreover, expressional investigations indicated that the family members of the clades L-type, G-I, G-IV and G-V were responsive to both bacterial and fungal infection. Based on qRT-PCR analysis, the expressions of PGSC0003DMP400055136 and PGSC0003DMP400067047 were strongly induced in all treatments by both Fusarium sulphureum (Fs) and Phytophthora infestans (Pi) inoculation. The present study provides valuable information for LecRLKs gene family in potato genome, and establishes a foundation for further research into the functional analysis.

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Peer Review #1 of "Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.) (v0.1)"

10.7287/peerj.9310v0.1/reviews/1 ◽

2020 ◽

Keyword(s):

Solanum Tuberosum ◽

Peer Review ◽

Solanum Tuberosum L ◽

Genome Wide Analysis ◽

Lectin Receptor ◽

Genome Wide

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Peer Review #2 of "Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.) (v0.2)"

10.7287/peerj.9310v0.2/reviews/2 ◽

2020 ◽

Keyword(s):

Solanum Tuberosum ◽

Peer Review ◽

Solanum Tuberosum L ◽

Genome Wide Analysis ◽

Lectin Receptor ◽

Genome Wide

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Peer Review #2 of "Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.) (v0.1)"

10.7287/peerj.9310v0.1/reviews/2 ◽

2020 ◽

Keyword(s):

Solanum Tuberosum ◽

Peer Review ◽

Solanum Tuberosum L ◽

Genome Wide Analysis ◽

Lectin Receptor ◽

Genome Wide

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Genome-Wide Identification and Expression Analysis of the Class III Peroxidase Gene Family in Potato (Solanum tuberosum L.)

Frontiers in Genetics ◽

10.3389/fgene.2020.593577 ◽

2020 ◽

Vol 11 ◽

Author(s):

Xuanshong Yang ◽

Jiazheng Yuan ◽

Wenbin Luo ◽

Mingyue Qin ◽

Jiahan Yang ◽

...

Keyword(s):

Solanum Tuberosum ◽

Gene Family ◽

Solanum Tuberosum L ◽

Pcr Analysis ◽

Class Iii ◽

Protein Motifs ◽

Real Time Quantitative Pcr ◽

Gene Pairs ◽

Genome Wide ◽

Class Iii Peroxidases

Class III peroxidases (PRXs) are plant-specific enzymes and play important roles in plant growth, development and stress response. In this study, a total of 102 non-redundant PRX gene members (StPRXs) were identified in potato (Solanum tuberosum L.). They were divided into 9 subfamilies based on phylogenetic analysis. The members of each subfamily were found to contain similar organizations of the exon/intron structures and protein motifs. The StPRX genes were not equally distributed among chromosomes. There were 57 gene pairs of segmental duplication and 26 gene pairs of tandem duplication. Expression pattern analysis based on the RNA-seq data of potato from public databases indicated that StPRX genes were expressed differently in various tissues and responded specifically to heat, salt and drought stresses. Most of the StPRX genes were expressed at significantly higher levels in root than in other tissues. In addition, real-time quantitative PCR (qRT-PCR) analysis for 7 selected StPRX genes indicated that these genes displayed various expression levels under abiotic stresses. Our results provide valuable information for better understanding the evolution of StPRX gene family in potato and lay the vital foundation for further exploration of PRX gene function in plants.

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Genomic regions of Solanum tuberosum L. associated with the tuber eye depth

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj20.638 ◽

2020 ◽

Vol 24 (5) ◽

pp. 465-473

Author(s):

I. V. Totsky ◽

I. V. Rozanova ◽

A. D. Safonova ◽

A. S. Batov ◽

Yu. A. Gureeva ◽

...

Keyword(s):

Solanum Tuberosum ◽

Solanum Tuberosum L ◽

Snp Markers ◽

Potato Genome ◽

Potato Species ◽

Area 5 ◽

High Level ◽

Genomic Regions ◽

Academy Of Sciences ◽

Eye Depth

Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber’s eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the “eye depth” trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1–48.9 Mb). The results of localization in the region 48.1–48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber’s eye depth were studied in the SolTub_3.0 potato genome assembly (https:// plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber’s eye depth.

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Genome-Wide Association Mapping of Late Blight Tolerance Trait in Potato (Solanum tuberosum L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.714575 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fang Wang ◽

Meiling Zou ◽

Long Zhao ◽

Zhiqiang Xia ◽

Jian Wang

Keyword(s):

Solanum Tuberosum ◽

Late Blight ◽

Potato Breeding ◽

Genome Wide Association Study ◽

Solanum Tuberosum L ◽

Potato Cultivars ◽

Genome Wide Association ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome

Uncovering the genetic basis and optimizing the late blight tolerance trait in potatoes (Solanum tuberosum L.) are crucial for potato breeding. Late blight disease is one of the most significant diseases hindering potato production. The traits of late blight tolerance were evaluated for 284 potato cultivars to identify loci significantly associated with the late blight tolerance trait. Of all, 37 and 15 were the most tolerant to disease, and 107 and 30 were the most susceptible. A total of 22,489 high-quality single-nucleotide polymorphisms and indels were identified in 284 potato cultivars. All the potato cultivars were clustered into eight subgroups using population structure analysis and principal component analysis, which were consistent with the results of the phylogenetic tree analysis. The average genetic diversity for all 284 potato cultivars was 0.216, and the differentiation index of each subgroup was 0.025–0.149. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about 0.9 kb. A genome-wide association study using a mixed linear model identified 964 loci significantly associated with the late blight tolerance trait. Fourteen candidate genes for late blight tolerance traits were identified, including genes encoding late blight tolerance protein, chitinase 1, cytosolic nucleotide-binding site–leucine-rich repeat tolerance protein, protein kinase, ethylene-responsive transcription factor, and other potential plant tolerance-related proteins. This study provides novel insights into the genetic architecture of late blight tolerance traits and will be helpful for late blight tolerance in potato breeding.

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Agrobacterium-mediated Genetic Transformation for Local Cultivars of Potato (Solanum tuberosum L.) Using Marker Genes

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v20i2.6894 ◽

1970 ◽

Vol 20 (2) ◽

pp. 145-155 ◽

Cited By ~ 1

Author(s):

Rita Sarah Borna ◽

M. I. Hoque ◽

R. H. Sarker

Keyword(s):

Solanum Tuberosum ◽

Genetic Transformation ◽

Solanum Tuberosum L ◽

In Vitro Regeneration ◽

Direct Regeneration ◽

Pcr Analysis ◽

Marker Genes ◽

Transformation Rate ◽

Best Responses

Genetic transformation using nodal and internodal segments from three economically important potato (Solanum tuberosum L.) varieties namely, Diamant, Cardinal and Granola was conducted using an Agrobacterium tumefaciens strain LBA4404 harbouring binary plasmid pBI12 containing the GUS and nptII genes. Node and internodal segments were used for direct regeneration as well as regeneration with the intervention of callus. best responses were obtained for direct regeneration of shoots when the explants were cultured on MS supplemented with 4.0 mg/l BAP +1.0 mg/l IAA, 1.5 mg/l BAP + 0.5 mg/l IAA and 5.0 mg/l BAP +1.0 mg/l IAA in Diamant, Cardinal and Granola, respectively. In Diamant spontaneous in vitro microtuberization was obtained from these proliferated shoots. Further culturing of these in vitro grown green microtubers regenerated a large number of shoots on MS containing 4.0 mg/l BAP +1.0 mg/l IAA. By combining the best treatments, this protocol yielded an average transformation rate of 87% of treared explants. Stable expression of GUS gene was visualized in the various parts of transformed shoots through histochemical assay. Genomic DNA was isolated from transformed shoots and stable integration of the GUS and nptII genes was confirmed by PCR analysis. Key words: Potato, in vitro regeneration, transformation D.O.I. 10.3329/ptcb.v20i2.6894 Plant Tissue Cult. & Biotech. 20(2): 145-155, 2010 (December)

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In vitro Regeneration and Agrobacterium-mediated Transformation of Potato (Solanum tuberosum L.) Cultivars Grown in Mexico

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v22i2.14193 ◽

2013 ◽

Vol 22 (2) ◽

pp. 93-105 ◽

Cited By ~ 1

Author(s):

Rose Onamu ◽

Juan P Legaria ◽

Jaime C Sahagún ◽

José L Rodríguez ◽

Joel N Pérez

Keyword(s):

Solanum Tuberosum ◽

Solanum Tuberosum L ◽

In Vitro Regeneration ◽

Potato Cultivars ◽

Pcr Analysis ◽

Nptii Gene ◽

Histochemical Assay ◽

Gus Histochemical Assay ◽

Binary Plasmid

Prior to Agrobacterium-mediated genetic transformation in vitro regeneration protocol was established for three potato cultivars (Alfa, Cambray Rosa Morelos and Atlantic) grown in Mexico using leaf, node and internodal explants. Regeneration protocol was developed with or without the intervention of callus. Two potato cultivars, namely, Cambray Rosa Morelos and Alpha were transformed using Agrobacterium tumefaciens strain LBA4404 harboring binary plasmid pBI121 containing the GUS and nptII genes. GUS histochemical assay and PCR analysis were conducted on rooted shoots grown in media without hormones but supplemented with antibiotics. Transformed shoots tested positive through GUS histochemical assay and integration of nptII gene was confirmed by PCR analysis DOI: http://dx.doi.org/10.3329/ptcb.v22i2.14193 Plant Tissue Cult. & Biotech. 22(2): 93-105, 2012 (December)

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