INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE

59-70

Authors: Puji Lestari, Habib Rijzaani, Dani Satyawan, Anneke Anggraeni, Dwinita W. Utami, Ida Rosdianti, Muchamad Lutfi and I Made Tasma

Single nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight "Ongole Grade" (OG) beef cattle and 20 "Holstein Friesian" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmenta-tion, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia.

79-86

Authors: Amran Muis, Nurnina Nonci and Marcia B. Pabendon

The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI) between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r) at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.

11-20

Authors: U.D. Chavan, S.S. Patila, B. Dayakar Rao and J.V. Patil

The present study was undertaken with the objective to standardise procedures for preparation of semolina (rava) from sorghum, to identify the best genotype for preparation of semolina and to study the nutritional quality parameters of semolina. For processing of sorghum, ten varieties and five hybrids were used for preparation of semolina and their products. A process has been standardized for semolina preparation using ultra grinding mill from sorghum grain. The semolina yield ranged from 46.51% to 54.29%. Hybrid CSH-15R gave the highest yield of semolina (54.29%). Starch content in semolina ranged from 59.93% to 66.43%. The new genotypes Phule Vasudha, Phule Yashoda and M 35-1 showed higher levels of starch content as compared to the other genotypes. The Phule Vasudha and Selection-3 showed higher levels of total soluble sugars in grains, as well as in semolina than the other genotypes. Phule Maulee gave higher level of crude fibre content (3.12%). The amino acid profile of sorghum grain and semolina showed very minor differences in the content due to the processing of sorghum grains into various products like semolina. The new genotypes of rabi sorghum showed comparable results for the mineral with that of hybrids. The organoleptic properties of the sweet (shira), upama and idali prepared from semolina were judged on the basis of colour, texture and appearance, flavour, taste and overall acceptability of the products using semi-trained judges and 1 to 9 hedonic scales. All products prepared from semolina were like very much and gave highest rating of more than 8 hedonic scales. While considering the yield of semolina from sorghum grains as well as their nutritional composition and organoleptic properties of the niche products (shira, upama, idali) prepared from them, the varieties Phule Vasudha and Phule Yashoda were the best one as compared to the other varieties and hybrids and overall varieties were better than the hybrids.

31-38

Authors: Kusdianawati, Apon Zaenal Mustopa, Suharsono, Bugi Ratno Budiarto, Fatimah and Hasim Danuri

Plantaricin is one of bacteriocins that have the potential to be used as food preservative. Plantaricin is safe for human consumption because it can be easily degraded by proteolytic enzymes. The objective of this study was to express and purify recombinant pre-mature peptide of plantaricin F from Lactobacillus plantarum S34 in Escherichia coli. Plantaricin gene-specific primer was used to obtain pln F structural gene amplicon from L. plantarum S34. This amplicon was cloned in pET32a vector and expressed in E. coli BL21 (DE3) pLysS. Pre-mature plantaricin F peptide was expressed as Histagged-fusion protein and separated by Co2+-chelating affinity chromatography. L. plantarum S34-derived pre-mature plantaricin F peptide fused with thioredoxin-(His)6tag had successfully been expressed in E. coli BL21 (DE3) pLysS using pET32a as an expression vector. The fused recombinant pln F as pre-mature state expressed had a molecular mass of +24 kDa, meanwhile the fused recombinant that contained only the leader peptide of pln F appeared as +20 kDa based on SDS-PAGE separations. The optimal production of fused recombinant pln F as soluble fraction was obtained when culture condition was added with 0.5 mM of IPTG and incubated at 22°C for 5 hours (OD~1). Furthermore, the expression of fused recombinant pln F as its pre-mature peptide pointed out that the pln F’s leader peptide could be proteolytically cleaved by a system in heterologous cells. Overall, heterologous pln F production as pre-mature peptide fused with thioredoxin-(His)6tag had been well established. From this research, we expect plantaricin F can be expressed and purified in E. coli.