Article
Plant Sciences
Zoe Andrijanic, Nelson Nazzicari, Hrvoje Sarcevic, Aleksandra Sudaric, Paolo Annicchiarico, Ivan Pejic
Summary: This study investigates the genetic diversity and structure of European soybean cultivars and American introductions registered in Europe, supporting optimal exploitation of genetic resources. Results show that the European soybean gene pool still has sufficient diversity due to differences in historical breeding practices and relatively short breeding period in Europe.
Article
Plant Sciences
Liubin Wang, Hanshuo Xun, Shirin Aktar, Rui Zhang, Liyun Wu, Dejiang Ni, Kang Wei, Liyuan Wang
Summary: Tea plants are an important economic crop globally, but the purity and authenticity of tea varieties have posed challenges in germplasm conservation and promotion. This study developed core SNP markers to accurately identify germplasm and analyze genetic relationships in tea plants. Based on whole-genome data, cultivars were divided into three groups: Assam type (CSA), Chinese type (CSS), and transitional type. Yunnan Province was identified as the primary center of CSA origin, while east China (primarily Zhejiang and Fujian provinces) was likely the area of origin and domestication of CSS. Additionally, 45 core SNP markers were developed, providing a molecular basis for identifying superior tea germplasm and facilitating breeding work.
Article
Plant Sciences
Mbali Thembi Gumede, Abe Shegro Gerrano, Assefa Beyene Amelework, Albert Thembinkosi Modi
Summary: This study assessed the genetic diversity and population structure of 90 cowpea accessions using SNP markers. The results showed that cowpea has high tolerance to heat and drought stresses, making it important for improving crop production resilience. The study also revealed low genetic diversity and high homozygosity among cowpea accessions.
Review
Plant Sciences
Stylianos Tympakianakis, Emmanouil Trantas, Evangelia V. V. Avramidou, Filippos Ververidis
Summary: The contribution of vine cultivation to human welfare and civilization has been significant, with a wide array of genetic variants used for cultivation. Understanding the origin and relationships among cultivars is of interest for phylogenetics and biotechnology. Molecular markers and next generation sequencing technologies have advanced the study of Vitis germplasm.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Paul Kitenge Kimwemwe, Chance Bahati Bukomarhe, Edward George Mamati, Stephen Mwangi Githiri, Rene Mushizi Civava, Jacob Mignouna, Wilson Kimani, Mamadou Fofana
Summary: This study assessed the genetic diversity and population structure of 94 rice genotypes from the Democratic Republic of Congo using high-quality DArTseq-based SNP markers. The results revealed high genetic diversity and significant population structure, which are crucial for breeding programs, conservation efforts, and the development of sustainable agriculture.
Article
Plant Sciences
Yanyan Wang, Hongkun Lv, Xiaohua Xiang, Aiguo Yang, Quanfu Feng, Peigang Dai, Yuan Li, Xun Jiang, Guoxiang Liu, Xingwei Zhang
Summary: This study used genotyping-by-sequencing to develop SNP markers for rapid and accurate identification of cigar tobacco varieties. Analysis of 113 cigar tobacco accessions showed complex genetic backgrounds. The research provides a scientific basis for screening high-quality cigar tobacco germplasm and genetic breeding work.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
L. R. Hu, D. Li, Q. Chu, Y. C. Wang, L. Zhou, Y. Yu, Y. Zhang, S. L. Zhang, T. Usman, Z. Q. Xie, S. Y. Hou, L. Liu, W. H. Shi
Summary: This study aimed to develop a SNP panel for parentage testing in the crossbred population, which consists of 50 highly informative SNPs. The SNP system provides sufficient and reliable information for parentage testing in Simmental and Holstein crossbred population, with minor allele frequency averaging 0.43 and cumulative probability of exclusion meeting high standards.
Article
Biotechnology & Applied Microbiology
Zhenhua Luo, Zien Chen, Mengyun Liu, Li Yang, Zhimin Zhao, Depo Yang, Ping Ding
Summary: The study found significant genetic variation in phenotypic, chemical, and SNP markers of Morinda officinalis How (MO). Different populations showed low genetic differentiation, mainly within populations. Cluster analysis based on morphology and oligosaccharide data revealed three distinct groups, consistent with SNP analysis, all correlated with geographical origin.
Article
Plant Sciences
Abraham Akpertey, Francis K. Padi, Lyndel Meinhardt, Dapeng Zhang
Summary: Accurate genotype identification is crucial for breeding new varieties of Coffea canephora L. with tolerance to biotic and abiotic stresses. This study validated SNP markers, uncovering mislabeling in genetic material and parentage errors. Analysis revealed significant genetic divergence among different populations of C. canephora genotypes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Horticulture
R. Sudha, M. K. Rajesh, V. Niral, K. Samsudeen, Sandip Shil, S. Ramchander, Y. Diwakar
Summary: A study on the genetic diversity and population structure of 16 coconut accessions from the International Coconut Genebank for South Asia and the Middle East (ICG-SAME) in India revealed high genetic diversity. The analysis used 35 SSR loci and found that the accessions exhibited different numbers of alleles, indicating potential for marker-assisted selection in coconut.
SCIENTIA HORTICULTURAE
(2023)
Article
Plant Sciences
Xi-ou Xiao, Ning Zhang, Hui Jin, Huaijun Si
Summary: This study evaluated the genetic diversity and population structure of 135 autotetraploid potatoes using SLAF-seq methods. Analysis of 3,397,137 high-quality SNPs revealed that the classification of these potatoes based on SNP profiles did not correlate with their geographical origins. Furthermore, 71 PARMS-SNP markers were successfully used to analyze 190 autotetraploid potato varieties. Overall, these novel SNP markers provide a solid foundation for potato genetic diversity analysis, DUS testing, and plant variety protection.
Article
Plant Sciences
Ali Khadivi, Farhad Mirheidari, Younes Moradi, Simin Paryan
Summary: This study assessed the morphological and pomological diversity among 81 accessions of Prunus microcarpa and revealed significant diversity in traits. The results have important implications for the conservation and breeding efforts of P. microcarpa.
Article
Horticulture
Kanamon Riangwong, Chatree Saensuk, Mutiara K. Pitaloka, Reajina Dumhai, Vinitchan Ruanjaichon, Theerayut Toojinda, Samart Wanchana, Siwaret Arikit
Summary: In this study, the genetic background, population structure, and genetic relationships among longan cultivars in Thailand were analyzed using genotyping-by-sequencing. The results showed that the longan accessions could be classified into four subpopulations and seven admixed genotypes. The study also revealed a high degree of genetic variation among the longan accessions and provided useful information for managing longan germplasm and genetic improvement.
Article
Genetics & Heredity
Misteru Tesfaye, Tileye Feyissa, Teklehaimanot Hailesilassie, Selvaraju Kanagarajan, Li-Hua Zhu
Summary: This study investigated the genetic diversity and population structure of Ethiopian mustard (Brassica carinata) genotypes of different origins using high-throughput single nucleotide polymorphism (SNP) markers. The results revealed two distinct subpopulations, with the majority of accessions clustered in one subpopulation mainly obtained from specific regions. The analysis showed high genetic variation within populations and low genetic differentiation between populations, indicating the presence of gene flow and weak geographical structure. The study provides important information for future breeding and conservation efforts of B. carinata.
Article
Genetics & Heredity
Muhammad Ahmad Yahaya, Hussein Shimelis, Baloua Nebie, Chris Ochieng Ojiewo, Abhishek Rathore, Roma Das
Summary: This study assessed the genetic diversity and population structure of 200 sorghum accessions using diversity arrays technology (DArT)-derived single nucleotide polymorphism (SNP) markers. The results showed a high level of genetic diversity among the accessions, which will be useful for enhancing sorghum breeding programs in West Africa by developing new gene pools and novel genotypes. Several distantly related sorghum accessions were identified, indicating the wide genetic diversity within the crop.
Article
Plant Sciences
Jason D. Zurn, John L. Norelli, Sara Montanari, Richard Bell, Nahla V. Bassil
Article
Multidisciplinary Sciences
Gina M. Sideli, Annarita Marrano, Sara Montanari, Charles A. Leslie, Brian J. Allen, Hao Cheng, Patrick J. Brown, David B. Neale
Review
Plant Sciences
Vance M. Whitaker, Steven J. Knapp, Michael A. Hardigan, Patrick P. Edger, Janet P. Slovin, Nahla V. Bassil, Timo Hytonen, Kathryn K. Mackenzie, Seonghee Lee, Sook Jung, Dorrie Main, Christopher R. Barbey, Sujeet Verma
HORTICULTURE RESEARCH
(2020)
Article
Forestry
Jason D. Zurn, April Nyberg, Sara Montanari, Joseph Postman, David Neale, Nahla Bassil
TREE GENETICS & GENOMES
(2020)
Article
Genetics & Heredity
Jonathan R. Nelson, Sujeet Verma, Nahla V. Bassil, Chad E. Finn, James F. Hancock, Glenn S. Cole, Steven J. Knapp, Vance M. Whitaker
Summary: The study identified two major QTLs enhancing resistance to charcoal rot, as well as a novel locus in hybrid varieties. These findings are of significance for DNA-informed breeding for resistance to charcoal rot in cultivated strawberries.
G3-GENES GENOMES GENETICS
(2021)
Article
Evolutionary Biology
Noemie Valenza-Troubat, Elena Hilario, Sara Montanari, Peter Morrison-Whittle, David Ashton, Peter Ritchie, Maren Wellenreuther
Summary: The aquaculture industry is rapidly growing, but has been slow to implement genomic techniques. This study on captive-bred F-1 silver trevally in New Zealand used genomics to analyze pedigree structure, genetic diversity, and growth patterns. Results showed potential for genetic improvement in economically important traits, making silver trevally a promising species for selective breeding.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Genetics & Heredity
Noemie Valenza-Troubat, Sara Montanari, Peter Ritchie, Maren Wellenreuther
Summary: This study identified quantitative trait loci and single nucleotide polymorphism markers associated with growth in trevally using quantitative trait locus mapping and genome-wide association studies. The results revealed genetic hot spots involved in growth and demonstrated the power of combining these two approaches for identifying and validating loci controlling complex traits.
G3-GENES GENOMES GENETICS
(2022)
Article
Multidisciplinary Sciences
Mandie Driskill, Katie Pardee, Kim E. Hummer, Jason D. Zurn, Keenan Amundsen, Annette Wiles, Claudia Wiedow, Josef Patzak, John A. Henning, Nahla Bassil
Summary: Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations. In this study, we developed two fingerprinting sets for hop: a 9-SSR fingerprinting set containing high-core repeats that can be run in a single PCR reaction and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs).
Article
Genetics & Heredity
Matthew R. Willman, Jill M. Bushakra, Nahla Bassil, Chad E. Finn, Michael Dossett, Penelope Perkins-Veazie, Christine M. Bradish, Gina E. Fernandez, Courtney A. Weber, Joseph C. Scheerens, Lisa Dunlap, Jonathan Fresnedo-Ramirez
Summary: The analysis of the genetic variation and stability of black raspberry traits provides insights into improving black raspberry germplasm and cultivars.
Article
Plant Sciences
Molla F. Mengist, Hamed Bostan, Domenico De Paola, Scott J. Teresi, Adrian E. Platts, Gaetana Cremona, Xinpeng Qi, Ted Mackey, Nahla Bassil, Hamid Ashrafi, Lara Giongo, Rubina Jibran, David Chagne, Luca Bianco, Mary A. Lila, Lisa J. Rowland, Marina Iovene, Patrick P. Edger, Massimo Iorizzo
Summary: Understanding the recombination behavior in polyploidy species is crucial for genetic discoveries. This study focused on blueberry, a tetraploid species, and investigated its genetic behavior using cytogenetics and high-density genetic maps. The study revealed the presence of an autotetraploid behavior and a translocation affecting chromosome pairing and recombination. No other structural genomic divergences were detected, providing valuable resources for future genetic and comparative genomic studies.
Review
Plant Sciences
Nick W. Albert, Massimo Iorizzo, Molla F. Mengist, Sara Montanari, Juan Zalapa, Andrew Maule, Patrick P. Edger, Alan E. Yocca, Adrian E. Platts, Boas Pucker, Richard Espley
Summary: The genus Vaccinium L. (Ericaceae) contains premium berryfruit crops, which are associated with various potential health benefits attributed to their high concentrations of flavonoids. Recent progress in Vaccinium genomics and genetics, as well as functional data on flavonoid regulation, have furthered our understanding of crop improvement and flavonoid biosynthesis. This update highlights the significant gains in genomic tools and functional analysis, using Vaccinium as an example.
Article
Biodiversity Conservation
Kim E. Hummer, Nahla Bassil, Jason D. Zurn, Beatrice Amyotte
Summary: This study evaluates the diversity of 284 strawberry cultivars through phenotype analysis and reveals a wide range of genetic variation. Some cultivars exhibit desirable traits such as high-quality fruits, early fruit ripening, or high numbers of daughter plants. The data provide valuable information for breeders, producers, and geneticists.
PLANTS PEOPLE PLANET
(2023)
