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Functional Polymorphism in Lycopene Beta-Cyclase Gene As a Molecular Marker to Predict Bixin Production in Bixa Orellana L

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Functional Polymorphism in Lycopene Beta-Cyclase Gene As a Molecular Marker to Predict Bixin Production in Bixa Orellana L Mol Breeding (2016) 36:135 DOI 10.1007/s11032-016-0555-y Functional polymorphism in lycopene beta-cyclase gene as a molecular marker to predict bixin production in Bixa orellana L. (achiote) Jose´ Abraham Trujillo-Hdz . Yair Ca´rdenas-Conejo . Pedro Escobar Turriza . Margarita Aguilar-Espinosa . Victor Carballo-Uicab . Luz Elena Garza-Caligaris . Luca Comai . Renata Rivera-Madrid Received: 26 February 2016 / Accepted: 2 September 2016 / Published online: 13 September 2016 Ó Springer Science+Business Media Dordrecht 2016 Abstract Bixin is an apocarotenoid obtained from variation in sixteen achiote accessions divided into the seed aril of Bixa orellana L., a tropical plant three groups according to contrasting traits, such as known as achiote in Mexico. This compound is the flower colour, fruit colour and bixin production. Using second most commonly used natural colouring for a combination of single-strand conformational poly- food and pharmaceutical industries. B. orellana is an morphism techniques and the sequencing of polymor- outcrossing species that displays high genetic vari- phic bands, we identified several single-nucleotide ability. Recently, the colour traits of sexual organs polymorphisms that divided the accessions into three were associated with the biosynthesis and accumula- haplotypes. Surprisingly, we observed that these three tion of bixin in mature seeds. Herein, we describe a haplotypes were consistent with the same three groups new approach for genotype–phenotype association by previously characterized by phenotypic traits. We surveying lycopene beta-cyclase (Bob-LCY1) gene derived a putative sequence for the Bob-LCY1 gene and surveyed the variations in this sequence. The heterozygosity of Bob-LCY1 alleles resulted in a Electronic supplementary material The online version of higher bixin content, likely associated with heterosis this article (doi:10.1007/s11032-016-0555-y) contains supple- for this metabolite. These findings augment the mentary material, which is available to authorized users. J. A. Trujillo-Hdz Y. Ca´rdenas-Conejo L. E. Garza-Caligaris P. E. Turriza M.Á Aguilar-Espinosa Á e-mail: [email protected] V. Carballo-UicabÁ L. E. Garza-CaligarisÁ R. Rivera-Madrid R. Rivera-Madrid (Á&) Á e-mail: [email protected] Centro de Investigacio´n Cientı´fica de Yucata´n A.C., Calle 43 No. 130, Col. Chuburna´ de Hidalgo, 97200 Me´rida, L. Comai Yucata´n, Mexico Genome Center, University of California, e-mail: [email protected] Davis, CA 95616, USA Y. Ca´rdenas-Conejo e-mail: [email protected] e-mail: [email protected] Present Address: P. E. Turriza Y. Ca´rdenas-Conejo e-mail: [email protected] Laboratorio de Bioingenierı´a, Universidad de Colima, Km. 9 M. Aguilar-Espinosa carretera Coquimatla´n-Colima, 28400 Coquimatla´n, Colima, e-mail: [email protected] Mexico V. Carballo-Uicab e-mail: [email protected] 123 135 Page 2 of 15 Mol Breeding (2016) 36:135 toolbox available for the selection and genetic et al. 2006; Valdez-Ojeda et al. 2010; Rodrı´guez-A´ vila improvement of B. orellana and provide a reliable et al. 2011). However, genetic selection based on phenotype–genotype association method for commer- sexual traits is difficult because the first flowering cial varietal selection, contributing to the development occurs in the third or fourth year after seed germina- of laboratory techniques to identify desirable traits of tion, followed by the annual flowering. Thus, a commercial plant species. molecular marker that could be used in young individuals to detect more productive plants would Keywords Annatto Bob-LCY1 gene Carotenoids be an important tool to improve field yields. Á Á Á SNP SSCP Heterosis Carotenoids are metabolites widely distributed in Á Á plants, contributing to the flavour, colour and/or aroma of the flowers and fruits (Moise et al. 2014; Nisar et al. 2015). In both plants and algae, the carotenoid Introduction pathway involves the cyclization of lycopene. Both a- and b-cyclase are needed for the biosynthesis of a- Achiote or Bixa orellana L. (locally known as carotene, which contains an e- (produced by a- ‘achiote’) is a perennial tree, native to the Neotropics cyclase) and a b-ionone ring (produced by b-cyclase), (Arce 1999) and the only cultivated species in the while b-carotene is produced only by the enzyme Bixaceae family (Ambro´sio Moreira et al. 2015). This lycopene-b-cyclase (b-LCY) (Cunningham et al. species has one of the lowest estimates for the amount 1996; Cunningham and Gantt 1998; Yuan et al. DNA among angiosperms, 4C = 0.78 pg with 2015). Carotenoids can also be cleaved at any of their 2n = 14 chromosomes (Hanson et al. 2001; De conjugated double bonds, resulting in a diverse set of Almeida et al. 2006). Bixa orellana L. was domesti- apocarotenoids (Auldridge et al. 2006) that can be cated in the Neotropics, although it is not clear where modified through dioxygenases, hydroxylases and or from which wild populations, and there is evidence epoxidases to produce physiologically important b- that Bixa urucurana Willd. is a subspecies of B. apocarotenoids, hormones such as abscisic acid orellana L. and likely the wild ancestor of cultivated (ABA) and strigolactones. In addition, apocarotenoid annatto or achiote (Ambro´sio Moreira, et al. 2015). modification can produce pigments such as crocetin Bixin is a natural colouring apocarotenoid derived and aromatic compounds, such as b-cyclocitral, a- and from the carotenoid biosynthesis pathway (Jako et al. b-damascenone, geranial, genaryl acetone, b-ionone, 2002; Bouvier et al. 2003). This molecule accumulates which are also commercially valuable products (Pfan- in the seed aril of B. orellana L. and is primarily used der and Schurtenberger 1982; Bouvier et al. 2003; as a colouring for dairy products, drinks and in the Frusciante et al. 2014; Nisar et al. 2015; Yuan et al. pharmaceutical industry (Giuliano et al. 2003). Addi- 2015). tionally, achiote seeds are the basic ingredients of a Bixa orellana produces bixin, an orange-red apoc- condiment used to prepare traditional dishes in arotenoid that accumulates in high concentrations and Mexico and other parts of the world (Godoy- accounts for 80 % of the total carotenoids present in Herna´ndez 2000; Avendan˜o-Arrate et al. 2012). seeds (Rivera-Madrid et al. 2006). Using a heterolo- Nevertheless, the production and trade of this com- gous system, previous studies have shown that pound are affected by the heterogeneity of bixin levels lycopene is transformed via a series of reactions, accumulated in the mature seeds of different plant involving a CCD4 dioxygenase enzyme (BoLCD), an varieties, reflecting the high genetic variability of this aldehyde dehydrogenase (BoBADH) and a methyl- species (Rivera-Madrid et al. 2006). Given the transferase (BoBMT), into bixin and bixin dimethyl economic potential of bixin, the early identification ester (Bouvier et al. 2003). of promising plants in breeding programmes would be The analysis of B. orellana gene transcripts encod- advantageous. Previous studies aimed at genetic ing carotenoid biosynthesis enzymes revealed that improvement have identified the phenotypic traits of PDS, b-LCY and e-LCY genes are highly regulated at achiote plants associated with differential pigment different stages of plant development and in plant accumulation in mature seeds, such as the colour of the accessions with different flower and fruit colours flower and fruit and pod dehiscence (Rivera-Madrid (Rodrı´guez-A´ vila et al. 2011). Thus, in two accessions 123 Mol Breeding (2016) 36:135 Page 3 of 15 135 of achiote differing in pigment content, Bob-LCY1 yellow dehiscent pods (Fig. 1). The young leaves were mRNA expression was correlated with carotene harvested from all accession plants and immediately accumulation (Rodrı´guez-A´ vila et al. 2011). Addi- stored in liquid nitrogen, transported to the laboratory tionally, in some plants, such as capsicum, water- and stored at -80 °C for subsequent analyses. melon, papaya and maize, DNA sequence polymorphisms in cyclase genes are associated with Determination of the bixin content the pigment phenotype (Bang et al. 2007; Ha et al. 2007; Harjes et al. 2008; Devitt et al. 2010). Based on The bixin contents in mature seeds called stage 3 (S3) these observations, the aim of the present study was to were spectrophotometrically quantified. This protocol investigate the existence of polymorphisms in the was specifically developed for B. orellana seeds Bob-LCY1 gene in different achiote accessions and (Mckeown and Mark 1962) using a formula consid- test a potential correlation to bixin levels. Here, we ering the extinction coefficient of chloroform. Pigment identify molecular markers using single-strand con- was extracted from the dried seeds of three biological formation polymorphism (SSCP) and DNA sequenc- replicates using chloroform (5 ml CHCl3 per 100 mg) ing, showing that polymorphism at Bob-LCY1 is for 30 min, and each sample was measured in associated with colour and bixin yield. triplicate. The bixin content was measured at 404 and 500 nm using a spectrophotometer (DU6-650 Beckman) and calculated using the formula according Materials and methods to McKeown and Mark (1962). An analysis of variance was carried out on the data Achiote plant accessions obtained using Statgraphics and complete randomiza- tion. Duncan multiple comparison tests (n = 3; Sixteen B. orellana individuals from the germplasm p B 0.5) were performed on the variables. Values bank located in CRUPY (Centro Regional Universi- labelled with the same letter are not significantly tario de la Peninsula de Yucatan, Mexico) were chosen different. for this study based on the associations observed previously between the plant colour traits and bixin Isolation and cloning of the lycopene beta-cyclase accumulation in mature seeds (Rivera-Madrid et al. Bob-LCY1 gene 2006; Valdez-Ojeda et al. 2010; Rodrı´guez-A´ vila et al. 2011). These plants were originally collected from To isolate and verify the Bob-LCY1 cDNA sequence Yaxcaba, Cooperativa and Chicxulub Pueblo (the (KT359004) in annatto identified by Ca´rdenas-Conejo achiote plantation of the ‘La Extra’ Company), from et al.
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