Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees.

Kittipat Ukoskit,Sithichoke Tangphatsornruang,Gunlayarat Bhusudsawang,Ratchanee Rattanawong,Thitaporn Phumichai,Wirulda Pootakham

doi:10.3390/plants10071440

Kittipat Ukoskit, Sithichoke Tangphatsornruang + Show 4 more

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https://doi.org/10.3390/plants10071440

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Abstract

Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.

Highlights

Girth growth of the rubber tree, Hevea brasiliensis (Willd.ex Adr.de Juss.) Muell
We developed a set of intron length polymorphism markers (ILP) markers from candidate genes involved in secondary growth and performed candidate gene association mapping for girth growth in Amazonian accessions
Our study showed that the cost-effective method of ILP gene-based markers can assist in identification of single nucleotide polymorphism (SNP) in the candidate gene associated with girth growth

Summary

Introduction

Girth growth of the rubber tree, Hevea brasiliensis (Willd.ex Adr.de Juss.) Muell. Arg., is the most important indicator of the maturity of the plantation, on which the harvesting of latex is based. Wood derived from the trunk of the rubber tree, harvested during periodic replanting, has emerged as an important raw material, especially in counties where logging of the natural forest is restricted. Breeding for girth growth is time-consuming, as the rubber tree has a long juvenile period, non-synchronous flowering, low fruit setting, and a heterozygous nature. Propagation of new varieties requires a minimum of 20–25 years of experimentation. To improve the rubber productivity, a deeper knowledge of the genetic factors responsible for variation in girth growth is necessary

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