Article
Plant Sciences
Zhen Li, Lan Yun, Zhiqi Gao, Tian Wang, Xiaomin Ren, Yan Zhao
Summary: This study analyzed the genetic diversity and population structure of Psathyrostachys juncea using molecular markers, and evaluated the genetic differentiation related to tillering traits. The results showed that the overall genetic relationship of P. juncea individuals was relatively close, and there was a significant correlation between genetic relationship and geographical distribution.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Horticulture
Yangmin Zhong, Yuan Cheng, Meiying Ruan, Qingjing Ye, Rongqing Wang, Zhuping Yao, Guozhi Zhou, Jia Liu, Jiahong Yu, Hongjian Wan
Summary: This study detected a large number of SSRs from the pepper genome, designed 240 SSR primers, and identified 33 SSR markers with high polymorphism in 147 accessions from 25 countries. The dendrogram clustered these accessions into seven major groups, providing SSR molecular marker resources and insight into genetic diversity of C. frutescens.
Article
Agronomy
Xiaoguang Wang, Xiang Liu, Zhifeng Zhang, Ying Chen, Lu Bai, Yue Du, Shijie Zhang, Zhiguo Zhang, Kun He, Min Fan, Qiaoping Qin
Summary: Daylily cultivars were analyzed using SSR markers, with a total of 9139 loci detected. The study identified 30 polymorphic EST-SSR markers and found a total of 98 alleles. Cluster analysis showed two phylogenetic groups among daylilies and night lilies.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Qi Zhou, Peng-Yan Zhou, Wen-Tao Zou, Yin-Gang Li
Summary: High-throughput sequencing of the Phoebe bournei transcriptome led to the identification of novel SSR markers, and genetic analyses revealed significant genetic differences among populations, with the YS population from Jiangxi province showing the highest genetic diversity.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Plant Sciences
Wei Xu, Jiancheng Wang, Changyan Tian, Wei Shi, Lei Wang
Summary: This study developed a set of polymorphic microsatellite markers to analyze the genetic diversity of three populations of S. aralocaspica in Xinjiang, China. The genetic diversity of S. aralocaspica was found to be moderate to high, providing a valuable resource for future genetic studies and breeding programs of S. aralocaspica and other species in Suaeda.
Article
Agronomy
Haizheng Xiong, Yilin Chen, San-Ji Gao, Yong-Bao Pan, Ainong Shi
Summary: This study assessed the genetic diversity and population structure of 196 Saccharum accessions, including various species and hybrids, using multiple analysis methods. The results showed that different species of sugarcane merged together, and specific alleles were important for sugarcane breeding and species identification. These findings provide valuable information for future genetic research and utilization of sugarcane germplasm resources.
Article
Agronomy
Zihao Wang, Hao Zhang, Boqiang Tong, Biao Han, Dan Liu, Ping Zhang, Dechang Hu
Summary: The present study investigated the genetic diversity and structure of endangered Juglans mandshurica populations in China. The results showed relatively low genetic diversity in J. mandshurica populations in Shandong areas, with high gene flow among populations potentially due to long-distance pollen transmission. Cluster analysis divided the populations into two groups, and structure analysis suggested interspecific introgression between J. mandshurica and common walnuts.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Wanling Yang, Zhiyi Bai, Fuqiang Wang, Mingzhu Zou, Xinru Wang, Jiankun Xie, Fantao Zhang
Summary: The genetic diversity and population structure of Monochasma savatieri individuals from four provinces in China were examined using EST-SSR markers, revealing low genetic diversity among populations and little gene flow within populations. Individuals from Zhejiang province showed the highest genetic diversity among the four populations. The study provided insights for designing effective conservation strategies for M. savatieri.
Article
Genetics & Heredity
Karina Ustariz, Mulatu Geleta, Helena Persson Hovmalm, Rodomiro Ortiz
Summary: In this study, the genetic diversity of Festuca species in the highlands of Bolivia was evaluated using EST-SSR markers. The results showed low genetic differentiation between populations and the newly developed markers are highly valuable for assessing the genetic diversity of Bolivian fescues and related species.
Article
Forestry
Zhi Yao, Zhi Feng, Chunwen Wu, Longping Tang, Xiuzhong Wu, Dahua Chen, Qiye Wang, Kaifang Fan, Yiqiang Wang, Meng Li
Summary: This study investigates the genetic diversity of Ginkgo biloba populations using EST-SSR markers. The results show a high level of genetic diversity and the construction of a core collection comprising 27 genetic resources. The developed molecular markers will facilitate future breeding of Ginkgo biloba.
Article
Plant Sciences
Mengli Ma, Hengling Meng, En Lei, Tiantao Wang, Wei Zhang, Bingyue Lu
Summary: Amomum tsaoko is a medicinal and food dual-use crop belonging to the Zingiberaceae family. This study provides transcriptome data and newly developed EST-SSR markers for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.
Article
Agronomy
Mohammed I. Al-daej, Adel A. Rezk, Mohamed M. El-Malky, Tarek A. Shalaby, Mohamed Ismail
Summary: This paper assessed the genetic diversities of 12 rice genotypes using ISSR and SSR markers, and evaluated their agro-morphological traits. Association mapping revealed significant marker-trait associations, including traits related to grain yield and harvest. These findings can enhance future molecular-based rice-breeding programs.
Article
Plant Sciences
Jiwei Yin, Hong Zhao, Xingting Wu, Yingxue Ma, Jingli Zhang, Ying Li, Guirong Shao, Hairong Chen, Ruixi Han, Zhenjiang Xu
Summary: In this study, 23 core SSR markers were selected from 287 screened SSR markers for the identification and distinction of non-heading Chinese cabbage varieties. These markers showed high polymorphic information content and could distinguish 99.994% of the varieties tested. The combination of SSR markers and morphological characteristics further improved the efficiency of variety identification.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Niyan Xiang, Bojie Lu, Tao Yuan, Tiange Yang, Jiani Guo, Zhihua Wu, Hong Liu, Xing Liu, Rui Qin
Summary: This study made progress in the molecular genetics and evolution research of the unique Chinese plant Chrysosplenium macrophyllum through transcriptome sequencing and EST-SSR markers, and found a high level of genetic diversity in C. macrophyllum. These developed molecular markers will be significant for the study of genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.
Article
Agricultural Engineering
Mohan Lal, Sunita Munda, Sangeeta Bhandari, Samarjit Saikia, Twahira Begum, Sudin Kumar Pandey
Summary: This study assessed the genetic diversity of Solanum khasianum in India and found that the 180 lines with solasodine content >0.8% exhibited high genetic diversity. The analysis using SSR markers revealed geographical clustering and the construction of a dendrogram. Furthermore, molecular variance analysis, principal component analysis, and genetic diversity parameter analysis were conducted, identifying SSR primers associated with solasodine content.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Ecology
Haruka Arashida, Haruka Odake, Masayuki Sugawara, Ryota Noda, Kaori Kakizaki, Satoshi Ohkubo, Hisayuki Mitsui, Shusei Sato, Kiwamu Minamisawa
Summary: Symbiosis between organisms influences evolution through adaptive changes in genome architectures. Interactions between soybeans and Bradyrhizobium involve IS-mediated duplications and deletions on symbiosis islands, with host plants selecting mutualistic variants from the pool of rhizobial populations. Homologous recombination between direct IS copies provides a natural mechanism for generating deletions and duplications in symbiosis islands.
Article
Biochemistry & Molecular Biology
Kenji Fujino, Kenta Shirasawa
Summary: This study elucidated the genetic population structure differences of rice landraces across Japan and identified two phases of differentiation, namely western to eastern and southern to northern phases. These differences may have facilitated the expansion of genetic diversity among local regions.
MOLECULAR GENETICS AND GENOMICS
(2022)
Letter
Plant Sciences
Kosuke Kuwabara, Shin-ichi Arimura, Kenta Shirasawa, Tohru Ariizumi
Article
Plant Sciences
Nozomi Obata, Hiroaki Tabuchi, Miyu Kurihara, Eiji Yamamoto, Kenta Shirasawa, Yuki Monden
Summary: This study used genome-wide association analysis to identify two genetic loci that regulate resistance to SRKN-SP2, which is the major race affecting sweetpotato production in Japan. Selective DNA markers were developed to screen for resistant plants, and the results showed a 70% probability of selecting SRKN-SP2-resistant plants when using these markers.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Tomonori Hirao, Koji Matsunaga, Kenta Shirasawa
Summary: This study constructed a high-density linkage map using genotyping-by-sequencing (GBS) and identified a key locus for resistance to pine wilt disease (PWD) caused by the pine wood nematode (PWN) in Pinus thunbergii. The findings provide valuable genetic information for resistance breeding programs in P. thunbergii.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Kenta Shirasawa, Munetaka Hosokawa, Yasuo Yasui, Atsushi Toyoda, Sachiko Isobe
Summary: We report the genome sequence of Capsicum annuum 'Takanotsume', a popular Japanese chili pepper landrace, obtained through long-read sequencing and optical mapping. The genome assembly consists of 12 pseudomolecules, covering 97.0% of the estimated genome size, and predicts 34,324 high-confidence genes. Comparative genomics analysis reveals nucleotide sequence and genome structure variations between 'Takanotsume' and related Capsicum species. This genome sequence data will accelerate pan-genomics and breeding of Capsicum, and facilitate the study of genetic mechanisms underlying important traits of 'Takanotsume'.
Article
Agronomy
Tomohito Ikegaya, Kenta Shirasawa, Kenji Fujino
Summary: Crop breeding programs can improve traits associated with desirable phenotypic characteristics in response to local environmental conditions. This study investigates the genetic differences underlying the traits of elite rice varieties and proposes the historical evolutionary process of cultivated rice based on genome sequencing and analysis. The fine mapping of a quantitative trait locus (qDTH3) associated with heading date narrows it down to a 158-kb region, and the phenotypic differences in qDTH3 in elite varieties may be derived from a different lineage split from the ancestor.
Article
Agronomy
Akio Ohyama, Hiroshi Matsunaga, Yasushi Kawasaki, Kenta Shirasawa, Satomi Negoro, Koji Miyatake, Hirotaka Yamaguchi, Tsukasa Nunome, Hiroyoshi Iwata, Hiroyuki Fukuoka, Takeshi Hayashi
Summary: Compared to a population derived from bi-parental crosses of pure lines, a customized experimental population derived from multi-parental crosses is advantageous for detecting multiple QTL alleles. A population of recombinant inbred lines (RILs) was established from crossing two commercial elite F-1 hybrid cultivars of tomato. Using two Bayesian mapping methods, significant QTLs for agricultural traits were detected in this population. A practical approach to genomic selection was presented based on the effects of the QTL alleles estimated in this study.
Article
Plant Sciences
Yusdar Mustamin, Turgut Yigit Akyol, Max Gordon, Andi Madihah Manggabarani, Yoshiko Isomura, Yasuko Kawamura, Masaru Bamba, Cranos Williams, Stig Uggerhj Andersen, Shusei Sato
Summary: This research found that winter survival was the direct target of selection during colonization of Japan by Lotus japonicus. Two candidate genes, FERONIA-receptor like kinase (LjFER) and a S-receptor-like kinase gene (LjLecRK), were identified to be required for non-acclimated freezing tolerance and exhibited haplotype-dependent cold-responsive expression. The study suggests that incorporating a conserved growth regulator gene, FER, and a receptor-like kinase gene, LecRK, into the cold-responsive genes contributed to freezing tolerance and local climate adaptation in L. japonicus, providing insights into the genetic mechanisms of perennial herb evolution.
Article
Horticulture
Ken Hoshikawa, Ya-Ping Lin, Roland Schafleitner, Kenta Shirasawa, Sachiko Isobe, Duc Chinh Nguyen, Ryo Ohsawa, Yosuke Yoshioka
Summary: This study analyzed the genetic diversity and population structure of 465 Amaranthus tricolor accessions held by the World Vegetable Center genebank. A total of 10,509 SNPs were found, and 5,638 SNPs without missing data were identified in 440 accessions. These findings contribute to the research and breeding of this species.
SCIENTIA HORTICULTURAE
(2023)
Article
Genetics & Heredity
Kenta Shirasawa, Ryohei Arimoto, Hideki Hirakawa, Motoyuki Ishimori, Andrea Ghelfi, Masami Miyasaka, Makoto Endo, Saneyuki Kawabata, Sachiko N. Isobe
Summary: In this study, a chromosome-scale de novo assembly of E. grandiflorum genome sequences was established using four genetic and genomic approaches. A total of 36,619 high-confidence genes were predicted, and whole-genome duplication was observed after the divergence between Gentianaceae and Rubiaceae. Genetic diversity analysis of commercial E. grandiflorum varieties was performed, and multiple variants were identified. This study provides valuable genomic resources for further genetic and genomic studies in Eustoma and the family Gentianaceae.
G3-GENES GENOMES GENETICS
(2023)
Article
Plant Sciences
Ken-ichi Kurotani, Hideki Hirakawa, Kenta Shirasawa, Yasuhiro Tanizawa, Yasukazu Nakamura, Sachiko Isobe, Michitaka Notaguchi
Summary: Nicotiana benthamiana is a widely used model plant for dicotyledonous angiosperms, but its previous reference genome was fragmented and hindered molecular genetic analysis. However, with improved genome assembly and annotation, N. benthamiana would become more accessible for research purposes.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Kenta Shirasawa, Roger Moraga, Andrea Ghelfi, Hideki Hirakawa, Hideki Nagasaki, Kioumars Ghamkhar, Brent A. Barrett, Andrew G. Griffiths, Sachiko N. Isobe
Summary: Subterranean clover (Trifolium subterraneum L., Ts) is an economically important forage legume with a compact genome. A new genome assembly TSUd_3.0 was generated using higher resolution sequence data, which improved prior genome assemblies. Molecular diversity analysis revealed copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. These findings provide a platform for future gene functional analysis and breeding strategies.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Takashi Akagi, Erika Varkonyi-Gasic, Kenta Shirasawa, Andrew Catanach, Isabelle M. Henry, Daniel Mertten, Paul Datson, Kanae Masuda, Naoko Fujita, Eriko Kuwada, Koichiro Ushijima, Kenji Beppu, Andrew C. Allan, Deborah Charlesworth, Ikuo Kataoka
Summary: Sex chromosome evolution is associated with sexual dimorphisms. We studied kiwifruit genomes and found recurrent sex chromosome turnovers in multiple lineages. The structural evolution of neo-Y chromosomes was driven by rapid transposable element insertions. Surprisingly, sexual dimorphisms were conserved across different species due to the pleiotropic effects of a single Y-chromosome-encoded sex-determining gene, Shy Girl.
Article
Genetics & Heredity
Daisuke Sekine, Satoshi Oku, Tsukasa Nunome, Hideki Hirakawa, Mai Tsujimura, Toru Terachi, Atsushi Toyoda, Masayoshi Shigyo, Shusei Sato, Hikaru Tsukazaki
Summary: This study presents a genome-wide marker design workflow for onions, which is applied in a high-throughput genotyping method using target amplicon sequencing. The efficiency of the method is evaluated by genotyping F-2 populations. The results show that our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions. However, there are missing or sparse marker regions in the resulting genetic linkage map, which need further improvement.
