EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety

Challenges and Opportunities for Indonesian Cocoa Development in the Era of Climate Change

In recent years, the area of cocoa plantations in Indonesia has tended to decline, one of which is attributed to climate change that threatens the sustainability of production; even though cocoa production and consumption have become popular globally, the consumer demand for cocoa products has also increased. Climate change causes increased air temperature, erratic rainfall patterns, increased sea level and surface temperature, and extreme weather. Cocoa requires an ideal rainfall of 1500–2500 mm/year and dry months (rainfall <60 mm) for about 1–3 month a year. Climate change can be a challenge for Indonesian cocoa development. Several efforts should be made to turn existing challenges into opportunities through appropriate technological inputs, such as the use of improved cocoa genetic resources (recommended clones) as well as improving nursery and field management practices, including shading and watering the seedlings, modification of growing media, mycorrhizal application, rainwater harvesting, and managing shade plants and intercropping

Whole chloroplast genome sequences contribute to phylogenetic relatedness and cultivar identification in cacao (Theobroma cacao L.)

Cacao (Theobroma cacao L.) is considered as economic importance crop playing a major role as source of chocolate industries for production of both chocolate candy and cocoa butter. Despite the advantages of cacao in industrial sector, understanding the global structure of cacao chloroplast genome plays a crucial role in explaining phylogenetic relationships and cultivar identification. This study aimed to perform phylogenetic analysis of cacao genotypes and develop DNA barcode markers using cacao chloroplast sequences. Chloroplast genome sequencing of two cacao genotypes (DR-1 and Sca-12) was conducted by the Illumina Miseq platform. Phylogenetic analysis of 12 cacao genotypes including two genotypes sequenced in this study (DR-1 and Sca-12) and ten genotypes previously sequenced (HQ336404, EET-64, ICS-01, ICS-06, ICS-39, Pentagonum, Sca-6, Stahel, Amelonado, and Criollo-22) showed a clear separation between bulk and fine types. This result demonstrated the usefulness of chloroplast sequences in revealing phylogenetic relatedness. Based on comparative chloroplast genome analysis of two cacao genotypes, DR-1 and Sca-12, three insertion/deletion (InDel) markers named as Theca_indel01, Theca_indel02, and Theca_indel03 which designed from the regions of trnA-UGC-rrn23, trnK-UUU-rps16, and rps16 intron, respectively were successfully developed to reveal barcode system for cacao genetic discrimination. Overall, these findings would provide valuable insight into the chloroplast genome structure of cacao plant, as well as information about the benefits of chloroplast sequences for constructing phylogenetic relationships and developing DNA barcode markers

Whole chloroplast genome sequences contribute to phylogenetic relatedness and cultivar identification in cacao (Theobroma cacao L.)

Cacao (Theobroma cacao L.) is considered as economic importance crop playing a major role as source of chocolate industries for production of both chocolate candy and cocoa butter. Despite the advantages of cacao in industrial sector, understanding the global structure of cacao chloroplast genome plays a crucial role in explaining phylogenetic relationships and cultivar identification. This study aimed to perform phylogenetic analysis of cacao genotypes and develop DNA barcode markers using cacao chloroplast sequences. Chloroplast genome sequencing of two cacao genotypes (DR-1 and Sca-12) was conducted by the Illumina Miseq platform. Phylogenetic analysis of 12 cacao genotypes including two genotypes sequenced in this study (DR-1 and Sca-12) and ten genotypes previously sequenced (HQ336404, EET-64, ICS-01, ICS-06, ICS-39, Pentagonum, Sca-6, Stahel, Amelonado, and Criollo-22) showed a clear separation between bulk and fine types. This result demonstrated the usefulness of chloroplast sequences in revealing phylogenetic relatedness. Based on comparative chloroplast genome analysis of two cacao genotypes, DR-1 and Sca-12, three insertion/deletion (InDel) markers named as Theca_indel01, Theca_indel02, and Theca_indel03 which designed from the regions of trnA-UGC-rrn23, trnK-UUU-rps16, and rps16 intron, respectively were successfully developed to reveal barcode system for cacao genetic discrimination. Overall, these findings would provide valuable insight into the chloroplast genome structure of cacao plant, as well as information about the benefits of chloroplast sequences for constructing phylogenetic relationships and developing DNA barcode markers

Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.

Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion

Yield performance and stability analysis of three cultivars of Gayo Arabica coffee across six different environments

The three cultivars of Gayo Arabica coffee (GAC) are distributed widely in the Gayo Highlands, Aceh Province, Indonesia, between 900 and 1,700 m above sea level (masl). The difference in altitude affects the yield and quality of coffee, and Arabica coffee has biennial bearing characteristics, so there are always annual yield fluctuations. This study aimed to determine the yield performance and stability level of the three GAC cultivars, Gayo 1, Gayo 2, and Gayo 3 (G3), across six different environments. The study used a randomized complete block design with three replications. The six environmental conditions are the combinations of two altitudes (900 and 1,500 masl) and 3 years of production (2019, 2020, and 2021). The estimation of coffee yields is based on the fruit value, which is calculated by the number of productive branches per tree, nodes per branch, berries per node, and the weight of a single cherry. An investigation of the genotype-by-environmental interaction using a combined analysis of variance and the yield performance and stability analysis performed using the Eberhart and Russell method, AMMI (additive main effects and multiplicative interaction) and GGE (genotype + genotype × environment) biplot analysis. Results showed that the yield performance of GAC was significantly affected by the interaction between genotype and environment. G3 was an ideal cultivar because it had high yield performance, was stable, and could adapt to broader environments in Gayo Highland. Therefore, G3 deserves high priority for Arabica coffee development in that region

Small-scale coffee farmers’ perception of climate-adapted attributes in participatory coffee breeding: A case study of Gayo Highland, Aceh, Indonesia

Small-scale coffee farming in Indonesia faces low productivity due to poor farming practices and low-quality planting materials. It highlights the need for improved coffee varieties that meet farmers’ preferences. Given the vulnerability of coffee farming to climate change, participatory breeding programs that involve collaboration between researchers and farmers to develop a climate-adapted variety are essential. This study used survey data from Gayo Highland, Aceh, Indonesia, to investigate farmers’ perception of the importance of climate-related attributes in a coffee variety, including those developed through a participatory breeding program, and the determinant factors. The result shows that farmers rated climate-related attributes as the least important (average score 0.36) compared to others, such as coffee productivity (1.57) and quality (1.22), resistance to pests and diseases (0.96), and input-use efficiency (0.57). This finding suggests a lack of awareness among farmers about the importance of climate issues in coffee farming. The estimation results also indicate that coffee extension activities have a negative association with farmers’ perceptions of the importance of climate attributes. This study recommends inclusive and targeted climate campaigns to increase farmers’ concern, awareness, and knowledge about the threats of climate change to coffee farming through strengthening advisory services

Comparison of 29 genes harboring BraTo-9 fragments with their homologous genes.

a<p>MITE position and alignment information can be found in Table S3.</p>b<p>Triplicated paralogs of <i>B. rapa</i> and orthologs from <i>A. thaliana</i> and <i>B. oleracea</i> were identified from BRAD annotation information. Bold indicates the gene with BraTo-9 insertion.</p

Identification of related empty sites by sequence comparison of MITE flanking regions with corresponding regions from <i>B. rapa</i> (A genome) or <i>B. oleracea</i> (C genome) homologs.

<p>The chromosome numbers and start positions of the sequences are indicated at the beginning of the sequence. TSD sequences are shown in bold.</p

MITE insertion polymorphism (MIP) analysis of 19 MITE families in the <i>Brassica</i> genome.

<p>The accessions used here: 1- <i>B. napus</i> (Tapidor), 2- <i>B. napus</i> (Ningyou 7), 3- <i>B. rapa</i> (Chiifu), 4- <i>B. rapa</i> (Kenshin), 5- <i>B. oleracea</i> (C1234), 6- <i>B. oleracea</i> (C1184), 7- <i>B. oleracea</i> (C1235), 8- <i>A. thaliana</i> (Columbia). M, molecular size marker. <i>Black</i> and <i>gray</i> arrowheads indicate the products with and without MITE insertion, respectively.</p