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SNP Variants of DELLA and Growth Regulating Factor Genes are Potentially Involved in Height in Coconut


Paper Type 
Contributed Paper
Title 
SNP Variants of DELLA and Growth Regulating Factor Genes are Potentially Involved in Height in Coconut
Author 
Kitti Walayaporn, Chutima Sonthirod, Wasitthee Kongkachana, Phakamas Phetchawang, Duangjai Sangsrakru, Nukoon Jomchai, Wirulda Pootakham, Sithichoke Tangphatsornruang, Tippaya Kraitong, Apichart Vanavichit and Suthasinee Somyong
Email 
suthasinee.som@nstda.or.th    
Abstract:

Coconut (Cocos nucifera L.), a plant in the Aracaceae family, is widely grown and consumed worldwide for many different utilities. Coconut is categorized in two main groups: dwarf and tall types, based on height. Harvesting of coconut fruits in the tall type is an inevitable obstacle for farmers. Hence, dwarf coconut varieties are cultivated instead of tall varieties. The study of height-related genes in coconut is also a necessity. The sequences of DELLA (CnDELLA1) and growth regulating factor (CnGRF1) genes were examined in this work because homologous genes have been found to associate with height in oil palm. PacBio SMRT sequencing technology was used to identify variations of these genes in 55 individual coconut trees. CnDELLA1 and CnGRF1 genes were successfully amplified by two PCR round amplification with sizes of around 1,671 and 1,003 base pairs (bp), respectively. A result of 1,201 and 626 gene sequences were derived from CnDELLA1 and CnGRF1, respectively, from all three coconut types to evaluate variations of these genes. Ten variant positions, comprised of 9 deletions and one SNP, were found for the CnDELLA1 gene while 4 deletions and 5 SNP variations were found for the CnGRF1 gene. Next, the genotypes of the six SNP variations were validated in 104 coconut trees to separate dwarf type from hybrid and tall types. After through-put genotyping of 5 targeted SNP markers by PACETM, mCnDELLA1_SNP1270 and mCnGRF1_SNP672 were found to potentially separate dwarf type from hybrid and tall types, based on their genotype distribution by a Chi-squared test, which was found to show a significant difference at p value < 0.01 between dwarf type, and hybrid and tall types. Contribution of these SNP markers to coconut height may be confirmed in the near future.

Start & End Page 
1271 - 1286
Received Date 
2021-01-25
Revised Date 
2021-08-22
Accepted Date 
2021-08-27
Full Text 
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Correspondence & Author Name 
Keyword 
coconut, DELLA, growth regulating factor, PacBio SMRT sequencing, height
Volume 
Vol.48 No.5 (September 2021)
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Chiang Mai Journal of Science

Faculty of Science, Chiang Mai University
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