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Non-tenera Contamination and the Economic Impact of SHELL Genetic Testing in the Malaysian Independent Oil Palm Industry

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Frontiers in Plant Science

Frontiers Media S.A.

oil palm, tenera, fruit form, shell, genetic testing

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      Abstract

      Oil palm (Elaeis guineensis) is the most productive oil bearing crop worldwide. It has three fruit forms, namely dura (thick-shelled), pisifera (shell-less) and tenera (thin-shelled), which are controlled by the SHELL gene. The fruit forms exhibit monogenic co-dominant inheritance, where tenera is a hybrid obtained by crossing maternal dura and paternal pisifera palms. Commercial palm oil production is based on planting thin-shelled tenera palms, which typically yield 30% more oil than dura palms, while pisifera palms are female-sterile and have little to no palm oil yield. It is clear that tenera hybrids produce more oil than either parent due to single gene heterosis. The unintentional planting of dura or pisifera palms reduces overall yield and impacts land utilization that would otherwise be devoted to more productive tenera palms. Here, we identify three additional novel mutant alleles of the SHELL gene, which encode a type II MADS-box transcription factor, and determine oil yield via control of shell fruit form phenotype in a manner similar to two previously identified mutant SHELL alleles. Assays encompassing all five mutations account for all dura and pisifera palms analyzed. By assaying for these variants in 10,224 mature palms or seedlings, we report the first large scale accurate genotype-based determination of the fruit forms in independent oil palm planting sites and in the nurseries that supply them throughout Malaysia. The measured non-tenera contamination rate (10.9% overall on a weighted average basis) underscores the importance of SHELL genetic testing of seedlings prior to planting in production fields. By eliminating non-tenera contamination, comprehensive SHELL genetic testing can improve sustainability by increasing yield on existing planted lands. In addition, economic modeling demonstrates that SHELL gene testing will confer substantial annual economic gains to the oil palm industry, to Malaysian gross national income and to Malaysian government tax receipts.

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      Most cited references 10

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      Assessing the redundancy of MADS-box genes during carpel and ovule development.

      Carpels are essential for sexual plant reproduction because they house the ovules and subsequently develop into fruits that protect, nourish and ultimately disperse the seeds. The AGAMOUS (AG) gene is necessary for plant sexual reproduction because stamens and carpels are absent from ag mutant flowers. However, the fact that sepals are converted into carpelloid organs in certain mutant backgrounds even in the absence of AG activity indicates that an AG-independent carpel-development pathway exists. AG is a member of a monophyletic clade of MADS-box genes that includes SHATTERPROOF1 (SHP1), SHP2 and SEEDSTICK (STK), indicating that these four genes might share partly redundant activities. Here we show that the SHP genes are responsible for AG-independent carpel development. We also show that the STK gene is required for normal development of the funiculus, an umbilical-cord-like structure that connects the developing seed to the fruit, and for dispersal of the seeds when the fruit matures. We further show that all four members of the AG clade are required for specifying the identity of ovules, the landmark invention during the course of vascular plant evolution that enabled seed plants to become the most successful group of land plants.
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        Oil palm genome sequence reveals divergence of interfertile species in old and new worlds

        Oil palm is the most productive oil-bearing crop. Planted on only 5% of the total vegetable oil acreage, palm oil accounts for 33% of vegetable oil, and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8 gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators 1 , which are highly expressed in the kernel. We also report the draft sequence of the S. American oil palm Elaeis oleifera, which has the same number of chromosomes (2n=32) and produces fertile interspecific hybrids with E. guineensis 2 , but appears to have diverged in the new world. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations which restrict the use of clones in commercial plantings 3 , and thus helps achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.
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          MADS-box protein complexes control carpel and ovule development in Arabidopsis.

          The AGAMOUS (AG) gene is necessary for stamen and carpel development and is part of a monophyletic clade of MADS-box genes that also includes SHATTERPROOF1 (SHP1), SHP2, and SEEDSTICK (STK). Here, we show that ectopic expression of either the STK or SHP gene is sufficient to induce the transformation of sepals into carpeloid organs bearing ovules. Moreover, the fact that these organ transformations occur when the STK gene is expressed ectopically in ag mutants shows that STK can promote carpel development in the absence of AG activity. We also show that STK, AG, SHP1, and SHP2 can form multimeric complexes and that these interactions require the SEPALLATA (SEP) MADS-box proteins. We provide genetic evidence for this role of the SEP proteins by showing that a reduction in SEP activity leads to the loss of normal ovule development, similar to what occurs in stk shp1 shp2 triple mutants. Together, these results indicate that the SEP proteins, which are known to form multimeric complexes in the control of flower organ identity, also form complexes to control normal ovule development.
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            Author and article information

            Affiliations
            1Malaysian Palm Oil Board Kajang, Malaysia
            2Orion Genomics, LLC, St. Louis MO, USA
            3Orion Biosains Sdn Bhd Puchong, Malaysia
            4BALSA Group, St. Louis MO, USA
            Author notes

            Edited by: Rajeev K. Varshney, International Crops Research Institute for the Semi-Arid Tropics, India

            Reviewed by: Matthew R. Willmann, Cornell University, USA; Hui Wang, University of Georgia, USA

            *Correspondence: Rajinder Singh, rajinder@ 123456mpob.gov.my

            This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science

            Contributors
            Journal
            Front Plant Sci
            Front Plant Sci
            Front. Plant Sci.
            Frontiers in Plant Science
            Frontiers Media S.A.
            1664-462X
            21 June 2016
            2016
            : 7
            27446094
            4914825
            10.3389/fpls.2016.00771
            Copyright © 2016 Ooi, Low, Abdullah, Nookiah, Ting, Nagappan, Manaf, Chan, Halim, Azizi, Omar, Murad, Lakey, Ordway, Favello, Budiman, Van Brunt, Beil, Leininger, Jiang, Smith, Brown, Kuek, Bahrain, Hoynes-O’Connor, Nguyen, Chaudhari, Shah, Choo, Sambanthamurthi and Singh.

            This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

            Counts
            Figures: 5, Tables: 4, Equations: 0, References: 17, Pages: 13, Words: 0
            Categories
            Plant Science
            Original Research

            Plant science & Botany

            shell, tenera, fruit form, genetic testing, oil palm

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