Genetic mapping and variability of seven soybean simple sequence repeat loci

Morgante, Michèle; Rafalski, Antoni; Biddle, Phyllis; Tingey, Scott V.; Olivieri, A. M.

doi:10.1139/g94-109

Cited by 134 publications

(73 citation statements)

References 26 publications

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“…For a comparative analysis among the methods, genetic parameters such as average number of alleles per locus, allele frequency (p i ), expected heterozygosity (H), effective number of alleles per locus (ne) were calculated as described by Morgante et al (1994) (N/N-1), where N is the sample size (number of cultivars evaluated). This measure takes into account both number and frequency of alleles.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR marker systems

Maluf

Silvestrini

Ruggiero

et al. 2005

Sci. agric. (Piracicaba, Braz.)

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One of the greatest problems in Coffea arabica breeding is identifying precisely any inbred line, based only on botanical and agronomical descriptors, because of the reduced genetic variability of the species, close pedigree origin, which results in small phenotypic variation. Recently, molecular markers have been used for plant germplasm characterization and identification in several commercial species. This work evaluates the reliability of three marker systems: RAPD, AFLP and SSR, to characterize the genetic variability of commercially-used Coffea inbred lines developed by the Instituto Agronômico (IAC), and their potential for cultivar identification. All methods identified polymorphisms among the cultivars. The genetic diversity recognized by the methods is very similar, although is very narrow. RAPD and SSR marker systems grouped more efficiently the evaluated cultivars according to parental origin. None of the methods allowed inbred line identification. Therefore for varietal protection, it would be necessary using a combination of botanical, agronomical and molecular markers descriptors for precise cultivar identification. Key words: coffee, cultivar identification, molecular markers CARACTERIZAÇÃO DA DIVERSIDADE GENÉTICA DE LINHAGENS COMERCIAIS DE Coffea arabica ATRAVÉS DE MARCADORES MOLECULARES DO TIPO RAPD, AFLP E SSRRESUMO: A identificação de linhagens de Coffea arabica a partir de descritores botânicos e agronômicos é um problema para o desenvolvimento de cultivares. Basicamente, a limitada variação fenotípica observada em cultivares é o resultado de uma estreita variabilidade genética em C. arabica associada com uma origem genealógica próxima. Recentemente, os uso de marcadores moleculares tem contribuído para a caracterização e identificação de várias espécies de interesse comercial. O objetivo deste trabalho foi comparar a confiabilidade de três tipos de marcadores moleculares, RAPD, AFLP e SSR, para a caracterização da variabilidade genética e uma possível identificação de linhagens comerciais de Coffea desenvolvidas pelo IAC. Os métodos avaliados permitiram identificar polimorfismos entre cultivares. A variabilidade genética detectada por eles é muito semelhante, ainda que reduzida. Marcadores do tipo RAPD e SSR foram mais eficientes em análises de parentesco, e o agrupamento das linhagens correspondeu à sua origem genealógica. No entanto, nenhum dos métodos testados permitiu a identificação individual de linhagens. Neste caso, a utilização conjunta de descritores botânicos, agronômicos e marcadores moleculares é recomendada para a identificação precisa de linhagens, visando processos de proteção legal de cultivares de Coffea.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR marker systems

Maluf

Silvestrini

Ruggiero

et al. 2005

Sci. agric. (Piracicaba, Braz.)

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“…그러나, 인삼의 경우 외부 형태적 특성에 의한 유전자원의 평가는 유 전자형과 환경 간의 상호작용과 해가림 시설 등 재배방법에 따라서 표현형이 달라지기 때문에 적당하지 않다. 이러한 문 제점을 보완하기 위하여, 환경에 영향을 받지 않는 DNA 마 커를 이용한 유전적 다양성 분석과 품종 판별 에 관한 연구가 진행되어, 오이 (Bernet et al, 2003), 대청 , 유채 (Tommasini et al, 2003), 고추 (Kwon et al, 2005), 밀 (Noil et al, 2008), 사과 (Cho et al, 2010 (Wu and Tanksley, 1993;Saghai-Maroof et al, 1994;Morgante et al, 1995;Ogbonnaya et al, 2008).…”

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Analysis of Genetic Polymorphism of Korean Ginseng Cultivars and Foreign Accessions using SSR Markers

Bang¹,

Jo²,

Chung³

et al. 2011

Korean Journal of Medicinal Crop Science

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: In this study, simple sequence repeat (SSR) analyses were utilized for evaluation of genetic diversity and discrimination of 17 accessions. Five cultivars, which were developed from Korea, and 12 foreign accessions, which were collected from China, Japan, Russia and USA, were evaluated by nine markers out of 22 SSR markers. A total of 39 alleles were detected, ranging from 2 to 8, with an average of 4.3 alleles per locus. The expected heterozygosity and PIC values were 0.627 and 0.553, with a range from 0.21 (GB-PG-078) to 0.76 (GB-PG-142) and from 0.19 (GB-PG-078) to 0.70 (GB-PG-142), respectively. Four makers out of nine SSR markers, GB-PG-026, GB-PG-043, GB-PG-142 and GB-PG-177, were selected as key factors for discrimination of Korean ginseng cultivars and foreign accessions. All of Korean ginseng cultivars and foreign accessions were individually by the combination of four SSR markers. Consequently, the SSR markers developed in this study may prove useful for the evaluation of genetic diversity and discrimination of Korean ginseng cultivars and foreign accessions.

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“…It is well known that the soybean genome is relatively monomorphic due to the narrow genetic base of cultivated soybean and possibly due to the domestication process from G. soja (Morgante et al 1994;Powell et al, 1996b). Therefore, identification of hypervariable regions is of considerable interest.…”

Section: Resultsmentioning

confidence: 99%

“…More recent molecular marker data suggest that the limited genetic diversity of cultivated soybean (G. max) is due not only to selection during the breeding process but also due to its domestication from G. soja (Morgante et al, 1994;Powell et al, 1996b).…”

Section: Introductionmentioning

confidence: 99%

Sequence characterization of hypervariable regions in the soybean genome: leucine-rich repeats and simple sequence repeats

2000

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The genetic basis of cultivated soybean is rather narrow. This observation has been confirmed by analysis of agronomic traits among different genotypes, and more recently by the use of molecular markers. During the construction of an RFLP soybean map (Glycine soja x Glycine max) the two progenitors were analyzed with over 2,000 probes, of which 25% were polymorphic. Among the probes that revealed polymorphisms, a small proportion, about 0.5%, hybridized to regions that were highly polymorphic. Here we report the sequencing and analysis of five of these probes. Three of the five contain segments that encode leucine-rich repeat (LRR) sequence homologous to known disease resistance genes in plants. Two other probes are relatively AT-rich and contain segments of (A)n/(T)n. DNA segments corresponding to one of the probes (A45-10) were amplified from nine soybean genotypes. Partial sequencing of these amplicons suggests that deletions and/or insertions are responsible for the extensive polymorphism observed. We propose that genes encoding LRR proteins and simple sequence repeat region prone to slippage are some of the most hypervariable regions of the soybean genome.
A base genética da soja cultivada é relativamente estreita. Essa observação foi confirmada por análises de características agronômicas entre diferentes genótipos e, mais recentemente, pelo uso de marcadores moleculares. Durante a construção de um mapa de RFLP da soja (Glycine soja x Glycine max), os dois progenitores foram analisados com mais de 2000 sondas, das quais 25% eram polimórficas. Entre as sondas que revelaram polimorfismos, uma pequena proporção, cerca de 0,5%, hibridizou com regiões que eram altamente polimórficas. Neste trabalho, são apresentados o seqüenciamento e análise de cinco dessas sondas. Três dessas sondas contêm segmentos que codificam repetições ricas em leucina que são homólogas a genes de resistência a doenças já conhecidos em plantas. As duas outras sondas são relativamente ricas em AT e contêm segmentos do tipo (A)n/(T)n. Segmentos de DNA correspondentes a uma das sondas (A45-10) foram amplificados a partir de nove genótipos de soja. Seqüenciamento parcial desses amplicons sugere que deleções e/ou inserções são responsáveis pelo extensivo polimorfismo observado. Nós propomos que os genes que codificam proteínas com repetições ricas em leucina e regiões de seqüências repetidas simples, que são passíveis do fenômeno de slippage (deslizamento), estão entre as regiões mais variáveis do genoma da soja

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Genetic mapping and variability of seven soybean simple sequence repeat loci

Cited by 134 publications

References 26 publications

Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR marker systems

Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR marker systems

Analysis of Genetic Polymorphism of Korean Ginseng Cultivars and Foreign Accessions using SSR Markers

Sequence characterization of hypervariable regions in the soybean genome: leucine-rich repeats and simple sequence repeats

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