scholarly journals Genetic Diversity and Demographic History of Ganoderma boninense in Oil Palm Plantations of Sarawak, Malaysia Inferred from ITS Regions

2019 ◽  
Vol 7 (10) ◽  
pp. 464 ◽  
Author(s):  
Midot ◽  
Lau ◽  
Wong ◽  
Tung ◽  
Yap ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Oil Palm ◽  
Demographic History ◽  
Internal Transcribed Spacers ◽  
Economic Losses ◽  
Nucleotide Polymorphisms ◽  
Founder Population ◽  
Ganoderma Boninense ◽  
Single Nucleotide ◽  
Major Haplotype

Ganoderma boninense causes basal stem rot (BSR) and is responsible for substantial economic losses to Southeast Asia’s palm oil industry. Sarawak, a major producer in Malaysia, is also affected by this disease. Emergence of BSR in oil palm planted on peat throughout Sarawak is alarming as the soil type was previously regarded as non-conducive. Phylogenetic analysis indicated a single species, G. boninense as the cause of BSR in Sarawak. Information on evolutionary and demographic history for G. boninense in Sarawak inferred through informative genes is lacking. Hence, a haplotype study on single nucleotide polymorphisms in internal transcribed spacers (SNPs-ITS) of G. boninense was carried out. Sequence variations were analysed for population structure, phylogenetic and phylogeographic relationships. The internal transcribed spacers (ITS) region of 117 isolates from four populations in eight locations across Sarawak coastal areas revealed seven haplotypes. A major haplotype, designated GbHap1 (81.2%), was found throughout all sampling locations. Single nucleotide polymorphisms were observed mainly in the ITS1 region. The genetic structure was not detected, and genetic distance did not correlate with geographical distance. Haplotype network analysis suggested evidence of recent demographic expansion. Low genetic differences among populations also suggested that these isolates belong to a single G. boninense founder population adapting to oil palm as the host.

Single nucleotide polymorphisms in oil palm HOMOGENTISATE GERANYL-GERANYL TRANSFERASE promoter for species differentiation and TOCOTRIENOL improvement

Meta Gene ◽  
2021 ◽  
Vol 27 ◽  
pp. 100818
Author(s):  
Mohd Shahrul Nizwanshah Karim ◽  
Siti Nor Akmar Abdullah ◽  
Mas Muniroh Mohd Nadzir ◽  
Mahdi Moradpour ◽  
Noor Azmi Shaharuddin ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Oil Palm ◽  
Species Differentiation ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Genome resequencing reveals demographic history and genetic architecture of seed salinity tolerance in Populus euphratica

2020 ◽  
Vol 71 (14) ◽  
pp. 4308-4320 ◽  
Author(s):  
Huixia Jia ◽  
Guangjian Liu ◽  
Jianbo Li ◽  
Jin Zhang ◽  
Pei Sun ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Salinity Tolerance ◽  
Genetic Architecture ◽  
Demographic History ◽  
Populus Euphratica ◽  
Tectonic Deformation ◽  
Nucleotide Polymorphisms ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Climatic Fluctuations

Abstract Populus euphratica is a dominant tree species in desert riparian forests and possesses extraordinary adaptation to salinity stress. Exploration of its genomic variation and molecular underpinning of salinity tolerance is important for elucidating population evolution and identifying stress-related genes. Here, we identify approximately 3.15 million single nucleotide polymorphisms using whole-genome resequencing. The natural populations of P. euphratica in northwest China are divided into four distinct clades that exhibit strong geographical distribution patterns. Pleistocene climatic fluctuations and tectonic deformation jointly shaped the extant genetic patterns. A seed germination rate-based salinity tolerance index was used to evaluate seed salinity tolerance of P. euphratica and a genome-wide association study was implemented. A total of 38 single nucleotide polymorphisms were associated with seed salinity tolerance and were located within or near 82 genes. Expression profiles showed that most of these genes were regulated under salt stress, revealing the genetic complexity of seed salinity tolerance. Furthermore, DEAD-box ATP-dependent RNA helicase 57 and one undescribed gene (CCG029559) were demonstrated to improve the seed salinity tolerance in transgenic Arabidopsis. These results provide new insights into the demographic history and genetic architecture of seed salinity tolerance in desert poplar.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide
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