Development, identification and validation of CAPS marker for SHELL trait which governs dura, pisifera and tenera fruit forms in oil palm (Elaeis guineensis Jacq.).

B Kalyana Babu,P Naveen Kumar,D Ramajayam,G Ravichandran,R K Mathur,S Sparjan Babu,M V B Venu,Manoj Prasad

doi:10.1371/journal.pone.0171933

Abstract

The oil palm fruit forms (dura, pisifera and tenera) governed by the shell thickness gene (Sh) plays a major role in identification of fruit type and also influences palm oil yield. Identification of desired fruit type is a major asset to the breeders and oil palm workers for applications in breeding, seed certification and to reduce time, space and money spent on identification of fruit form. In the present study, we developed Sh gene specific primer pairs and bulk segregant analysis was done using 300 genomic and 8 genic SSR markers. We identified one cleaved amplified polymorphic site (CAPS) marker for differentiation of oil palm fruit type which produced two alleles (280 and 250bp) in dura genotypes, three alleles in tenera genotypes (550, 280, and 250bp) and one allele in pisifera genotypes (550bp). The shell allele sequencing results showed that two SNPs were present, of which SNP2 contributed for variation of fruit forms. The nucleotide ‘A’ was present in only dura genotypes, where as ‘T’ was present only in pisifera genotypes, which in turn led to the change of amino acid lysine to aspargine. The identified CAPS marker was validated on 300 dura, 25 pisifera and 80 tenera genotypes, 80 dura/ pisifera cross progenies and 60 lines of tenera/ tenera cross progeny. Association mapping of marker data with phenotypic data of eight oil yield related traits resulted in identification of seven significant QTLs by GLM approach, four by MLM approach at a significant threshold (P) level of 0.001. Significant QTLs were identified for fruit to bunch and oil to bunch traits, which explained R2 of 12.9% and 11.5% respectively. The CAPS marker used in the present study facilitate selection and timely distribution of desirable high yielding tenera sprouts to the farmers instead of waiting for 4–5 years. This saves a lot of land, time and money which will be a major breakthrough to the oil palm community.

Highlights

Oil palm (Elaeis guineensis Jacq.) belongs to the family Arecaceae which contributes nearly 40 percent of edible vegetable oil production throughout the world [1]
In order to find the markers linked to the SHELL thickness in oil palm, in the present study a three tier approach has been used
The SHELL gene is responsible for identification of oil palm fruit forms viz., dura, pisifera and tenera [3]

Summary

Introduction

Oil palm (Elaeis guineensis Jacq.) belongs to the family Arecaceae which contributes nearly 40 percent of edible vegetable oil production throughout the world [1]. The oil palm genotypes are divided into dura, pisifera and tenera forms based on the shell thickness, which is a monogenic and co-dominantly inherited trait. The tenera (T) genotype has thin shell which has 30% more mesocarp and oil production than dura and pisifera, which is generally produced as hybrid from cross between D and P. The tenera hybrid yields more oil and is the basis for commercial palm oil production in all the oil palm growing parts of the world. Identification of these three fruit forms is a challenging task for oil palm breeders and growers. The fruit form determination can be possible only after 4–5 years by dissection of the fruit based on the thickness of shell and fibre ring, which requires a lot of time and space

Methods

Results

Conclusion