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Stochastic alternative splicing is prevalent in mungbean ( <i>Vigna radiata</i> )
Satyawan, Dani,Kim, Moon Young,Lee, Suk‐,Ha BLACKWELL 2017 PLANT BIOTECHNOLOGY JOURNAL Vol.15 No.2
<P><B>Summary</B></P><P>Alternative splicing (AS) can produce multiple mature mRNAs from the same primary transcript, thereby generating diverse proteins and phenotypes from the same gene. To assess the prevalence of AS in mungbean (<I>Vigna radiata)</I>, we analysed whole‐genome RNA sequencing data from root, leaf, flower and pod tissues and found that at least 37.9% of mungbean genes are subjected to AS. The number of AS transcripts exhibited a strong correlation with exon number and thus resembled a uniform probabilistic event rather than a specific regulatory function. The proportion of frameshift splicing was close to the expected frequency of random splicing. However, alternative donor and acceptor AS events tended to occur at multiples of three nucleotides (i.e. the codon length) from the main splice site. Genes with high exon number and expression level, which should have the most AS if splicing is purely stochastic, exhibited less AS, implying the existence of negative selection against excessive random AS. Functional AS is probably rare: a large proportion of AS isoforms exist at very low copy per cell on average or are expressed at much lower levels than default transcripts. Conserved AS was only detected in 629 genes (2.8% of all genes in the genome) when compared to <I>Vigna angularis</I>, and in 16 genes in more distant species like soya bean. These observations highlight the challenges of finding and cataloguing candidates for experimentally proven AS isoforms in a crop genome.</P>
Seo Hyoseob,Kwon Hakyung,Satyawan Dani,Kim Moon Young,Ha Jungmin,Lee Suk-Ha 한국유전학회 2023 Genes & Genomics Vol.45 No.7
Background Flowering time is an important crop trait. Mungbean flowers do not flower simultaneously, leading to asynchronous pod maturity and laborious multiple harvests per individual plant. The genomic and genetic mechanisms of flowering in mungbean are largely unknown. Objective This study sought to discover new quantitative trait loci (QTLs) for days to first flowering in mungbean using a genome-wide association study (GWAS). Methods In total, 206 mungbean accessions collected from 20 countries were sequenced using genotyping by sequencing. A GWAS was conducted using 3,596 single nucleotide polymorphisms (SNPs) using TASSEL v5.2. Results Seven significant SNPs were associated with first flowering time. Based on the linkage disequilibrium (LD) decay distance, LD block was determined from upstream to downstream of each SNP up to 384 kb. The lead SNP (Chr2_51229568) was located in the DFF2-2 locus. Syntenic analysis between mungbean and soybean revealed the DFF2-2 locus had collinearity with soybean genomic regions containing flowering-related QTLs on Gm13 and Gm20. Conclusion Identification of flowering-related QTLs and SNPs is important for developing synchronous pod maturity and desirable flowering traits in mungbean.
Genetic diversity of <i>Jatropha curcas</i> collections from different islands in Indonesia
Anggraeni, Tantri Dyah Ayu,Satyawan, Dani,Kang, Yang Jae,Ha, Jungmin,Kim, Moon Young,Chitikineni, Annapurna,Varshney, Rajeev K.,Lee, Suk-Ha Cambridge University Press 2018 Plant genetic resources Vol.16 No.4
<B>Abstract</B><P><I>Jatropha curcas</I> L. is a potential bioenergy crop but has a lack of improved cultivars with high yields and oil content. Therefore, increasing our understanding of <I>J. curcas</I> germplasm is important for designing breeding strategies. This study was performed to investigate the genetic diversity and population structure of Indonesian <I>J. curcas</I> populations from six different islands. To construct a reference, we <I>de novo</I> assembled the scaffolds (N50 = 355.5 kb) using 182 Gb Illumina HiSeq sequencing data from Thai <I>J. curcas</I> variety Chai Nat. Genetic diversity analysis among 52 Indonesian <I>J. curcas</I> accessions was conducted based on yield traits and single nucleotide polymorphism (SNP) markers detected by mapping genotyping-by-sequencing reads from Indonesian population to Chai Nat scaffolds. Strong variation in yield traits was detected among accessions. Using <I>J. integerrima</I> as an outgroup, 13,916 SNPs were detected. Among <I>J. curcas</I> accessions, including accessions from other countries (Thailand, the Philippines and China), 856 SNPs were detected, but only 297 SNPs were detected among Indonesian <I>J. curcas</I> populations, representing low genetic diversity. Through phylogenetic and structural analysis, the populations were clustered into two major groups. Group one consists of populations from Bangka and Sulawesi in the northern part of Indonesia, which are located at a distance of 1572.59 km. Group two contains populations from islands in the southern part: Java, Lombok-Sumbawa, Flores and Timor. These results indicate that introduction of diverse <I>J. curcas</I> germplasms is necessary for the improvement of the genetic variation in the Indonesian collections.</P>
Information Technology Infrastructure for Agriculture Genotyping Studies
Pardamean, Bens,Baurley, James W.,Perbangsa, Anzaludin S.,Utami, Dwinita,Rijzaani, Habib,Satyawan, Dani Korea Information Processing Society 2018 Journal of information processing systems Vol.14 No.3
In efforts to increase its agricultural productivity, the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development has conducted a variety of genomic studies using high-throughput DNA genotyping and sequencing. The large quantity of data (big data) produced by these biotechnologies require high performance data management system to store, backup, and secure data. Additionally, these genetic studies are computationally demanding, requiring high performance processors and memory for data processing and analysis. Reliable network connectivity with large bandwidth to transfer data is essential as well as database applications and statistical tools that include cleaning, quality control, querying based on specific criteria, and exporting to various formats that are important for generating high yield varieties of crops and improving future agricultural strategies. This manuscript presents a reliable, secure, and scalable information technology infrastructure tailored to Indonesian agriculture genotyping studies.
Translational genomics for plant breeding with the genome sequence explosion
Kang, Yang Jae,Lee, Taeyoung,Lee, Jayern,Shim, Sangrea,Jeong, Haneul,Satyawan, Dani,Kim, Moon Young,Lee, Suk‐,Ha BLACKWELL 2016 PLANT BIOTECHNOLOGY JOURNAL Vol.14 No.4
<P><B>Summary</B></P><P>The use of next‐generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.</P>
Information Technology Infrastructure for Agriculture Genotyping Studies
Bens Pardamean,James W. Baurley,Anzaludin S. Perbangsa,Dwinita Utami,Habib Rijzaani,Dani Satyawan 한국정보처리학회 2018 Journal of information processing systems Vol.14 No.3
In efforts to increase its agricultural productivity, the Indonesian Center for Agricultural Biotechnology andGenetic Resources Research and Development has conducted a variety of genomic studies using highthroughputDNA genotyping and sequencing. The large quantity of data (big data) produced by thesebiotechnologies require high performance data management system to store, backup, and secure data. Additionally, these genetic studies are computationally demanding, requiring high performance processorsand memory for data processing and analysis. Reliable network connectivity with large bandwidth to transferdata is essential as well as database applications and statistical tools that include cleaning, quality control,querying based on specific criteria, and exporting to various formats that are important for generating highyield varieties of crops and improving future agricultural strategies. This manuscript presents a reliable, secure,and scalable information technology infrastructure tailored to Indonesian agriculture genotyping studies.
Ha, Jungmin,Shim, Sangrea,Lee, Taeyoung,Kang, Yang J.,Hwang, Won J.,Jeong, Haneul,Laosatit, Kularb,Lee, Jayern,Kim, Sue K.,Satyawan, Dani,Lestari, Puji,Yoon, Min Y.,Kim, Moon Y.,Chitikineni, Annapurna John Wiley and Sons Inc. 2019 Plant biotechnology journal Vol.17 No.2
<P><B>Summary</B></P><P><I>Jatropha curcas</I> (physic nut), a non‐edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of <I>J. curcas</I> var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up‐regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine <I>Jatropha</I> species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.</P>