Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

Rota, Mauricio La; Kantety, Ramesh V.; Yu, Ju‐Kyung; Sorrells, Mark E.

doi:10.1186/1471-2164-6-23

Cited by 244 publications

(146 citation statements)

References 37 publications

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“…The data analysis pipeline contained two main self‐developed programs: The first one demultiplexed the reads to each locus and sample with the sequences of the primer loci and index bases of samples added by PCR (Figure S1), and the second one identified alleles via a modified algorithm of MEGASAT (Zhan et al., 2016). The program is distinguished from previous software (Suez et al., 2015; Zhan et al., 2016) because it adopts the Sputnik algorithm (La Rota et al., 2005) to search the microsatellite repeat array. This characteristic enabled the program to function without background information, such as microsatellite sequences and repeat array flank sequences, and only primer sequences are needed to classify reads to loci and index bases for demultiplexing the reads to samples.…”

Section: Discussionmentioning

confidence: 99%

“…For SSRs, we used modified Sputnik (La Rota, Kantety, Yu, & Sorrells, 2005) to search di‐, tri‐, tetra‐, and pena‐nucleotide unit SSRs, and Primer3 (Untergasser et al., 2012) was then used to design the primers. For the SNPs, we first use Bowtie2 (Langmead & Salzberg, 2012) for mapping clean reads to transcripts and then called SNPs using SAMtools (Li et al., 2009).…”

Section: Methodsmentioning

confidence: 99%

“…We used a modified algorithm in the MEGASAT software (Zhan et al., 2016) to define the genotypes for each locus and individual. Compared with the original version of MEGASAT, we adopted the algorithm from Sputnik software (La Rota et al., 2005) to search the microsatellite repeat array. Each microsatellite repeat array was used as a different locus to avoid the length artifacts contributed by PCR errors and sequence indels of bases between microsatellites if an amplicon contained more than one microsatellite.…”

Section: Methodsmentioning

confidence: 99%

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De novo assembly and characterization of the Hucho taimen transcriptome

Tong

Xü

Zhang

et al. 2017

Ecology and Evolution

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Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA‐Seq is a useful tool for obtaining genetic information and developing genetic markers for nonmodel species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA‐Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high‐quality transcriptome with a N50 size of 1,060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein‐coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including eight salmonids and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: It possesses more immune‐related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids, and selective breeding for threatened taimen.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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De novo assembly and characterization of the Hucho taimen transcriptome

Tong

Xü

Zhang

et al. 2017

Ecology and Evolution

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“…There was a preponderance of AT, TA and AAG for di and trinucleotide motifs, similar to cotton ESTs (Park et al 2005) and Arabidopsis (Cardle et al 2000). However, other plant species such as wheat, rice and barley (La Rota et al 2005) differ in their lower frequency of these motifs and a higher frequency of CGC and CCG motifs. The bases C and G rarely cooccur in our SSR motifs and this may be a distinguishing feature between monocotyledonous and dicotyledonous plants.…”

Section: Discussionmentioning

confidence: 99%

Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends

Frelichowski¹,

et al. 2006

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Fine mapping and positional cloning will eventually improve with the anchoring of additional markers derived from genomic clones such as BACs. From 2,603 new BAC-end genomic sequences from Gossypium hirsutum Acala 'Maxxa', 1,316 PCR primer pairs (designated as MUSB) were designed to flank microsatellite or simple sequence repeat motif sequences. Most (1164 or 88%) MUSB primer pairs successfully amplified DNA from three species of cotton with an average of three amplicons per marker and 365 markers (21%) were polymorphic between G. hirsutum and G. barbadense. An interspecific RIL population developed from the above two entries was used to map 433 marker loci and 46 linkage groups with a genetic distance of 2,126.3 cM covering approximately 45% of the cotton genome and an average distance between two loci of 4.9 cM. Based on genome-specific chromosomes identified in G. hirsutum tetraploid (A and D), 56.9% of the coverage was located on the A subgenome while 39.7% was assigned to the D subgenome in the genetic map, suggesting that the A subgenome may be more polymorphic and recombinationally active than originally thought. The linkage groups were assigned to 23 of the 26 chromosomes. This is the first genetic map in which the linkage groups A01 and A02/D03 have been assigned to specific chromosomes. In addition the MUSB-derived markers from BAC-end sequences markers allows fine genetic and QTL mapping of important traits and for the first time provides reconciliation of the genetic and physical maps. Limited QTL analyses suggested that loci on chromosomes 2, 3, 12, 15 and 18 may affect variation in fiber quality traits. The original BAC clones containing the newly mapped MUSB that tag the QTLs provide critical DNA regions for the discovery of gene sequences involved in biological processes such as fiber development and pest resistance in cotton.

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“…Similarmente Aggarwal et al 15 Tanto para Iapar 59 e CaHT o motivo mais abundante foi da classe (AT) n como representado nas tabelas 2 e 3. Os resultados obtidos para ambas cultivares neste estudo reforçam o que foi descrito por La Rota et al 18 e Cardle et al 19 , no qual os motivos poli AT são os mais encontrados na maioria dos genomas de plantas. Além disso, a classe (AT) n foi um dos mais frequentes dinucleotídeos relatados por Aggarwall et al 15 .…”

Section: Resultsunclassified

Identificação e Caracterização de Microssatélites de Coffea arabica a partir de dados de sequenciamento de RNA e de BACs

Silva

Cação

Ivamoto

et al. 2013

BBR - Biochem. Biotechnol.

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RESUMO:O café é uma das principais commodities agrícolas comercializados. A estreita base genética de Coffea arabica tem-se refletido em diferentes formas. Além disso, em C. arabica, o desenvolvimento de novas cultivares é demorado. A utilização de marcadores moleculares como ferramenta para análises da diversidade e seleção de genótipos representa uma importante ferramenta para tentar diminuir tempo e custo de seleção do melhoramento de espécies perenes como C. arabica. Neste trabalho foi realizada identificação e análise in silico de SSR a partir de dados de RNA-seq de C. arabica-Iapar 59 e de sequenciamento de BACs de C. arabica HDT832/2. Para Iapar 59 foram analisados 77 contigs, encontrados 39 SSR's e desenhados 21 primers. Para HDT832/2 foram analisados também 77 contigs, encontrados 35 SSR's e desenhados 29 primers. Os motivos mais frequentes foram di, tri e tetra, sendo AT o mais frequente entre os genótipos. Esta busca de sequências repetitivas é de grande importância para futura validação e aumento desses marcadores para estudos de diversidade genética.PALAVRAS-CHAVE: marcadores SSR's, análise in silico, RNA-seq, cromossomo artificial de bactéria. INTRODUÇÃOO café é uma das principais commodities agroindustriais de países em desenvolvimento e uma das mais populares bebidas não alcoólicas. Seu consumo abrange regularmente 40% da população mundial 1 , sendo o Brasil e os Estados Unidos os dois maiores consumidores. O Brasil é também o maior produtor e exportador mundial de café, e a região centro-sul de minas gerais o maior estado produtor com 52,0% na produção nacional 2 . O cultivo no Brasil é em sua maior parte de C. arabica, com cerca de 70% da produção, e o restante de C. canephora (30%) 3 . Para assegurar o poder comercial competitivo do café no país, os programas de melhoramento genético estão sempre buscando soluções para fatores bióticos e abióticos que podem prejudicar a cafeicultura, assim como investir na produção de cultivares com sabor superior e qualidade diferencial. Além disso, os mercados exigem cada vez mais esforços para o desenvolvimento de cafés de melhor de qualidade 4 .Estudos anteriores sobre a caracterização do germoplasma de C. arabica, incluindo análises usando marcadores moleculares relataram a baixa diversidade genética de C. arabica tanto de genótipos selvagens como cultivados 5 . As justificativas para a estreita base de diversidade genética incluem a recente origem da espécie, sua reprodução preferencialmente autógama, e o limitado histórico de dispersão. Além disso, o café é uma cultura perene que exige três anos de crescimento, até a plena maturidade 6 , sendo preciso pelo menos 20 anos para obter uma nova cultivar. Entretanto a utilização de ferramentas como os marcadores moleculares é uma ótima opção, pois permitem acesso à variabilidade genética do cafeeiro e a escolha precoce de características de interesse com menor custo e tempo. Dentre os marcadores moleculares atualmente disponíveis, Simple Sequence Repeats (SSR's) ou microssatélites, são sequências de DNA compo...

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Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

Cited by 244 publications

References 37 publications

De novo assembly and characterization of the Hucho taimen transcriptome

De novo assembly and characterization of the Hucho taimen transcriptome

Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends

Identificação e Caracterização de Microssatélites de Coffea arabica a partir de dados de sequenciamento de RNA e de BACs

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