Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

Lu, Xianjun; Zhou, Hui; Pan, Yong‐Bao; Chen, C.Y.; Zhu, Jun; Chen, P.H.; Li, Y.-R.; Cai, Qingsheng; Chen, R.K.

doi:10.4238/2015.december.23.26

Cited by 15 publications

(15 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Since the information on ploidy levels of test ecotypes was not available, SSR fragments were analyzed following a dominant scoring scheme, as used for other polyploidy species [34][35][36][37]. ALS-Binary and Allelobin software [38,39] were used to convert allelic data to binary data (0, 1) where 0 and 1 represent absence and presence of an allele, respectively.…”

Section: Discussionmentioning

confidence: 99%

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

et al. 2017

View full text Add to dashboard Cite

Brachiaria grass is an emerging forage option for livestock production in Kenya. Kenya lies within the center of diversity for Brachiaria species, thus a high genetic variation in natural populations of Brachiaria is expected. Overgrazing and clearing of natural vegetation for crop production and nonagricultural uses and climate change continue to threaten the natural biodiversity. In this study, we collected 79 Brachiaria ecotypes from different parts of Kenya and examined them for genetic variations and their relatedness with 8 commercial varieties. A total of 120 different alleles were detected by 22 markers in the 79 ecotypes. Markers were highly informative in differentiating ecotypes with average diversity and polymorphic information content of 0.623 and 0.583, respectively. Five subpopulations: International Livestock Research Institute (ILRI), Kitui, Kisii, Alupe, and Kiminini differed in sample size, number of alleles, number of private alleles, diversity index, and percentage polymorphic loci. The contribution of within-the-individual difference to total genetic variation of Kenyan ecotype population was 81%, and the fixation index (F ST = 0.021) and number of migrant per generation (Nm = 11.58) showed low genetic differentiation among the populations. The genetic distance was highest between Alupe and Kisii populations (0.510) and the lowest between ILRI and Kiminini populations (0.307). The unweighted neighbor-joining (NJ) tree showed test ecotypes grouped into three major clusters: ILRI ecotypes were present in all clusters; Kisii and Alupe ecotypes and improved varieties grouped in clusters I and II; and ecotypes from Kitui and Kiminini grouped in cluster I. This study confirms higher genetic diversity in Kenyan ecotypes than eight commercial varieties (Basilisk, Humidicola, Llanero, Marandú, MG4, Mulato II, Piatá and Xaraés) that represent three species and one three-way cross-hybrid Mulato II. There is a need for further collection of local ecotypes and their morphological, agronomical, and genetic characterizations to support Brachiaria grass breeding and conservation programs.

show abstract

Section: Discussionmentioning

confidence: 99%

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Microsatellites have been used to evaluate crop germplasm and genetic diversity in several species, including rye [9], grape [10], sugarcane [11], rice [12], and olive [13]. Agrobiodiversity of fruit tree is of increasing concern mainly because repositories still remain a valuable source of allelic variation for many traits and can be exploited for breeding in the near future.…”

Section: Microsatellites Have a Series Of Characteristics That Make Tmentioning

confidence: 99%

Use of Microsatellites to Study Agricultural Biodiversity and Food Traceability

Bernardi¹,

Colli²,

Ughini³

et al. 2016

Microsatellite Markers

View full text Add to dashboard Cite

Molecular markers are useful tools for measuring the genetic diversity among agricultural species. In plants, microsatellites are still the most used markers for germplasm characterization, conservation, and traceability purposes, while in the livestock sector, although having represented the standard for at least two decades, they are still used only for minor farm animal species. In this work, together with a review on the use of microsatellites in livestock, we also illustrate the use of these markers for the characterization of agricultural diversity and food traceability through two case studies: (i) the analysis of genetic diversity in ancient fruit tree cultivars of apple (Malus × domestica Borkh.), pear (Pyrus communis L.), sweet cherry (Prunus avium L.), and sour cherry (Prunus cerasus L.) from Northern Italy and (ii) the molecular authentication of wheat food chain. In the former case, a high genetic variability as well as the presence of different ploidy levels were detected, while in the latter microsatellite markers were shown to be useful for traceability and product authentication along the whole food chain. Overall, the presented evidence confirms the versatility of microsatellites as markers for both agrobiodiversity characterization and food traceability in cultivated plants and farm animals.

show abstract

“…Simple sequence repeats (SSRs or microsatellites) are one of the most commonly used DNA molecular markers to determine genetic diversity between sorghum genotypes (Motlhaodi et al, 2014;Lu et al, 2015). Knowledge on genetic diversity and the phytochemical relationships among accessions in crop germplasm collections is essential for establishing, managing, and ensuring the long-term success of crop improvement programs (Gebhardt et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Chemical and genetic diversity of high-seed-yield sorghum (Sorghum bicolor M.) germplasms

Ryu

Kwon³

et al. 2016

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. This study evaluated the chemical and genetic diversity of high-seed-yield sorghum germplasms from Korea, the United States, and South Africa. We identified significant differences in the chemical contents of whole plants at the heading stage in all cultivars, including differences in crude protein, fat, fiber, ash, neutral detergent fiber, acid detergent fiber, mineral, and fatty acid contents. Our results suggest that Banwoldang is the most appropriate cultivar for roughage because of its high protein yield. We identified significant differences in the tannin, flavonoid, amylose, mineral, crude fat, fatty acid, and 3-deoxyanthocyanin contents in the whole grain from all cultivars, but not in the mineral or crude fat contents. Tannin levels were generally low. IS645 contained the highest levels of flavonoids and linolenic acid compounds, and Moktak had the highest amylose and deoxyanthocyanidin content in the grain. To assess genetic diversity, we used 10 simple sequence repeat (SSR) primer sets to identify 38 2 J. Ryu et al. Genetics and Molecular Research 15 (3): gmr.15038677 alleles with 3-8 alleles per locus. Based on phylogenetic analysis of the SSR markers, the sorghum cultivars were divided into three major groups. Comparison of clusters based on chemical compositions with those based on SSRs showed that the groups formed by the three native Korean cultivars clustered similarly in molecular dendrograms. Association analysis was conducted for the 10 SSR marker; 48 chemical and growth traits were present for two marker traits (seed color and whole plant fatty acid content) with significant marker-trait associations. These markers could be used to select sorghum cultivars for breeding programs.

show abstract

Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

Cited by 15 publications

References 27 publications

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers

Use of Microsatellites to Study Agricultural Biodiversity and Food Traceability

Chemical and genetic diversity of high-seed-yield sorghum (Sorghum bicolor M.) germplasms

Contact Info

Product

Resources

About