GROWTH AND EXPRESSION PATTERN OF GROWTH-RELATED GENES IN THE FAST-GROWING GIANT GOURAMI Osphronemus goramy

Growth improvement of the giant gourami through molecular assisted selection offers a breakthrough solution regarding the slow growth problem in culturing the fish species. However, gene molecular expression studies and gene mapping information are scarce for this species. This study aimed to evaluate the growth, expression of the growth-related genes and compare the gene expressions between fast-growing (FG) and slow-growing (SG) fish. The polymorphism screenings were also conducted within the GH sequence of the FG and SG populations. Fish growth was analyzed by measuring length and weight once a month. The expression levels of GH, IGF1, AMPK, ARS-I, ALT, and AST genes were analyzed using real-time PCR. Twenty-five days old fish were reared for 30 days. The fish were continuously reared separately based on their body weight (BW) for 85 days until reaching 140 days old. At the end of the rearing period, the BW growth rate of the FG population was 1.569-fold higher, and body length (BL) growth was 1.056-fold higher than the SG population. FG fish have higher gene expression than the SG fish, indicating the important role of gene expression in fish growth. The polymorphisms screening within the GH sequences showed no significant difference between FG and SG fish of giant gourami. These research results provide valuable information in developing the marker-assisted selection for growth traits in giant gourami.

Evaluation of the crossings between local and drought-tolerant rice varieties using simple sequence repeat (SSR) molecular marker

Two cultivars of local rice, namely Mentik Wangi and Mentik Susu, have been grown around west to south flank of Merapi volcano. They are highly valued for their good taste and cooking characteristics. An attempt to introduce drought-tolerant rice varieties has been conducted by crossing them with two sources, namely Kasalath and Bluebonnet. Molecular-assisted selection using a set of SSR markers was applied to check the F1 and F2 generation trueness and segregation. This research was conducted in the facilities of Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta. The research was a field experiment arranged in a completely randomized design, consisting of Mentik Wangi, Mentik Susu, Bluebonnet, and Kasalath, as well as their crossings’ F1 and F2 plants as treatments. The SSR markers used are RM72, RM228, RM518, and RM20(A). Polymorphism test of the parents showed that polymorphism exists between local and donor parents, thus these markers were considered eligible for the F1 and F2 tests. The heterozygous individuals of F1 were 75% for Bluebonnet × Mentik Wangi, 44.4% for Bluebonnet × Mentik Susu, and 46.7% for Mentik Wangi × Bluebonnet; all were consistent in every primer used. We could not confirm that the F2 populations showed segregation pattern that followed Mendelian segregation in some crosses due to too small size of the sample. Heterozygous individuals in F2 showed the differences pattern for each marker, indicating that the location of the SSR markers were far from each other in the genome.

Molecular Assisted Selection for Pollination-Constant and Non-Astringent Type without Male Flowers in Spanish Germplasm for Persimmon Breeding

Persimmon (Diospyros kaki Thunb) species is a hexaploid genotype that has a morphologically polygamous gyonodioecious sexual system. D. kaki bears unisexual flowers. The presence of male flowers resulted in the presence of seeds in the varieties. The fruits of persimmon are classified according to their astringency and the pollination events that produced seeds and modify the levels of astringency in the fruit. The presence of seeds in astringent varieties as pollination variant astringent (PVA), pollination variant non-astringent (PVNA) and pollination constant astringent (PCA) resulted in fruits not marketable. Molecular markers that allow selection of the varieties according to the type of flowers at the plantlet stage would allow selection of seedless varieties. In this study, a marker developed in D. lotus by bulk segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) markers, named DlSx-AF4, has been validated in a germplasm collection of persimmon, results obtained agree with the phenotype data. A second important trait in persimmon is the presence of astringency in ripened fruits. Fruits non-astringent at the ripen stage named pollination constant non-astringent (PCNA) are the objective of many breeding programs as they do not need removal of the astringency by a postharvest treatment. Astringency in the hexaploid persimmon is a dominant trait. The presence of at least one astringent allele confers astringency to the fruit. In this paper we checked the marker developed linked to the AST gene. Our goal has been to validate both markers in germplasm from different origins and to test the usefulness in a breeding program.

Developmental, morphological and molecular variation of commercial Ganoderma spp. accessions from southern Vietnam

Ho VT, Vo TNH, Le NG. 2019. Developmental, morphological and molecular variation of commercial Ganoderma spp. accessions from southern Vietnam. Biodiversitas 20: 3684-3689. In Vietnam, the market value of Ganoderma spp. increases markedly recently due to the high demand as an effective medicine. However, the breeding programs for this mushroom are still less effective due to the poor knowledge of genetic composition. This study was conducted to investigate the diversity of some commercial Ganoderma spp. accessions from southern Vietnam using both traditional techniques using developmental and morphological characterization, and molecular method using ISSR markers. A total of nine Ganoderma spp. samples were collected from production areas and research institutes in southern provinces of Vietnam and targeted for developmental and molecular characterization. Developmental and morphological variations among accessions were evaluation. In addition, 20 ISSR markers were also utilized for further understanding genetic composition of these mushrooms. The obtained measurement data show a large variation among the studied Ganoderma spp. accessions in term of mycelia growth, diameter, shape, and dried weight of fruiting bodies. Molecular data from 20 ISSR markers also supported genetic variation of the examined samples. Based on the results of this study, the samples of Ganoderma spp. accessions from southern Vietnam can be divided into two main groups which are not correlated to geographical locations of sample collection sites. The results are potential for classification and provide new insights for molecular assisted selection of Ganoderma spp.

Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing

Simple sequence repeats (SSRs) or microsatellite markers derived from expressed sequence tags (ESTs) are routinely used for molecular assisted-selection breeding, comparative genomic analysis, and genetic diversity studies. In this study, we investigated 54,546 ESTs for the identification and development of SSR markers in Pogostemon cablin (Patchouli). In total, 1219 SSRs were identified from 1144 SSR-containing ESTs. Trinucleotides (80.8%) were the most abundant SSRs, followed by di- (10.8%), mono- (7.1%), and hexa-nucleotides (1.3%). The top six motifs were CCG/CGG (15.3%), AAG/CTT (15.0%), ACC/GGT (13.5%), AGG/CCT (12.4%), ATC/ATG (9.9%), and AG/CT (9.8%). On the basis of these SSR-containing ESTs, a total of 192 primer pairs were randomly designed and used for polymorphism analysis in 38 accessions collected from different geographical regions of Guangdong, China. Of the SSR markers, 45 were polymorphic and had allele variations from two to four. Furthermore, a transferability analysis of these primer pairs revealed a 10–40% cross-species transferability in 10 related species. This report is the first comprehensive study on the development and analysis of a large set of SSR markers in P. cablin. These markers have the potential to be used in quantitative trait loci mapping, genetic diversity studies, and the fingerprinting of cultivars of P. cablin.