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1. De  novo chromosome level assembly of a plant genome from long read sequence data

Author:
Priyanka Sharma; Ardashir Kharabian Masouleh; Bruce Topp; Agnelo Furtado; Robert J. Henry
Source:
plant journal 2022 v.109 no.3 pp. 727-736
ISSN:
0960-7412
Subject:
chromosome mapping,   etc   ; DNA; Macadamia; telomeres;     Show all 4 Subjects
Abstract:
... Recent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. Chromosome level genome assemblies using sequence contigs generated from long read sequencing have involved the use of proximity analysis (Hi‐C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The develop ...
DOI:
10.1111/tpj.15583

2. Multi-algorithm cooperation in PnbHLH genes under Nitrogen stress

Author:
Caijuan Zhang; Tingting Zhang; Jianfen Zheng; Kaijing Yan; Zongsuo Liang; Pengguo Xia
Source:
Industrial crops and products 2022 v.183 pp. 114997
ISSN:
0926-6690
Subject:
chromosome mapping,   etc   ; Panax notoginseng; genes; nitrogen; people; phylogeny; China;     Show all 7 Subjects
Abstract:
... Panax notoginseng (Burkill) F. H. Chen ex C. H. increasingly entered into people's daily life, but its quality has been greatly affected in recent years. Panax notoginseng is one of the representatives of the ginseng plant of Araliaceae, which is an important and precious local medicinal material in China. Basic helix–loop–helix transcription factors play an irreplaceable position in the life of p ...
DOI:
10.1016/j.indcrop.2022.114997

3. A high-resolution consensus linkage map for barley based on GBS-derived genotypes

Author:
Amina Abed; Ana Badea; Aaron Beattie; Raja Khanal; James Tucker; François Belzile
Source:
Genome 2022 v.65 no.2 pp. 83-94
ISSN:
1480-3321
Subject:
chromosome mapping,   etc   ; barley; genetic recombination; genomics; genotyping by sequencing;     Show all 5 Subjects
Abstract:
... As genotyping-by-sequencing (GBS) is widely used in barley genetic studies, the translation of the physical position of GBS-derived SNPs into accurate genetic positions has become relevant. The main aim of this study was to develop a high-resolution consensus linkage map based on GBS-derived SNPs. The construction of this integrated map involved 11 bi-parental populations composed of 3743 segregat ...
DOI:
10.1139/gen-2021-0055

4. Genetic Map Construction, QTL Mapping, and Candidate Genes Screening of Grain Size Traits in Common Buckwheat (Fagopyrum esculentum M.)

Author:
Xiaomei Fang; Yuanli Zhang; Jingbin Cui; Lingqing Yue; Jianbo Tao; Yigang Wang; Ruifeng Zhang; Jiaqi Liu; Aohua Jiang; Jian Zhang; Renwu Ruan; Zelin Yi
Source:
Agronomy 2022 v.12 no.9 pp. -
ISSN:
2073-4395
Subject:
chromosome mapping,   etc   ; Fagopyrum esculentum; agronomy; buckwheat; genes; phenotype; pseudocereals; transcriptome; Ukraine;     Show all 9 Subjects
Abstract:
... Common buckwheat (Fagopyrum esculentum M.) is an important pseudo-cereal crop and contains an abundance of nutrients and bioactive compounds. However, the yield of buckwheat is low compared to that of other major crops. QTL mapping and candidate gene screening of grain size are very important for increasing production in common buckwheat through molecular breeding in the future. In the present stu ...
DOI:
10.3390/agronomy12092062

5. An Integrated Linkage Map of Three Recombinant Inbred Populations of Pea (Pisum sativum L.)

Author:
Chie Sawada; Carol Moreau; Gabriel H. J. Robinson; Burkhard Steuernagel; Luzie U. Wingen; Jitender Cheema; Ellen Sizer-Coverdale; David Lloyd; Claire Domoney; Noel Ellis
Source:
Genes 2022 v.13 no.2 pp. -
ISSN:
2073-4425
Subject:
chromosome mapping,   etc   ; Pisum sativum; cultivars; dissection; inbred lines; peas; population structure;     Show all 7 Subjects
Abstract:
... Biparental recombinant inbred line (RIL) populations are sets of genetically stable lines and have a simple population structure that facilitates the dissection of the genetics of interesting traits. On the other hand, populations derived from multiparent intercrosses combine both greater diversity and higher numbers of recombination events than RILs. Here, we describe a simple population structur ...
DOI:
10.3390/genes13020196

6. The construction of a high-density consensus genetic map for soybean based on SNP markers derived from genotyping-by-sequencing

Author:
Manel Fallah; Martine Jean; Vincent-Thomas Boucher St-Amour; Louise O'Donoughue; François Belzile
Source:
Genome 2022 v.65 no.8 pp. 413-425
ISSN:
1480-3321
Subject:
chromosome mapping,   etc   ; genome; genomics; genotyping by sequencing; single nucleotide polymorphism; soybeans;     Show all 6 Subjects
Abstract:
... Genetic linkage maps are used to localize markers on the genome based on the recombination frequency. Most often, these maps are based on the segregation observed within a single biparental population of limited size (n < 300) where relatively few recombination events are sampled and in which some genomic regions are monomorphic because both parents carry the same alleles. Together, these two limi ...
DOI:
10.1139/gen-2021-0054

7. Assemblies of the genomes of parasitic wasps using meta-assembly and scaffolding with genetic linkage

Author:
Kameron T Wittmeyer; Sara J Oppenheim; Keith R Hopper
Source:
G3 GenesGenomesGenetics pp. -
ISSN:
2160-1836
Subject:
chromosome mapping,   etc   ; Aphelinus; Aphidoidea; biological control; genes; host specificity; parasitoids; quantitative traits;     Show all 8 Subjects
Abstract:
... Safe, effective biological-control introductions against invasive pests depend on narrowly host-specific natural enemies with the ability to adapt to a changing environment. As part of a project on the genetic architectures of these traits, we assembled and annotated the genomes of two aphid parasitoids, Aphelinus atriplicis and Aphelinus certus. We report here several assemblies of A. atriplicis ...
DOI:
10.1093/g3journal/jkab386
CHORUS:
10.1093/g3journal/jkab386

8. Comparative QTL analysis in peach ‘Earlygold’ F2 and backcross progenies

Author:
Naveen Kalluri; Iban Eduardo; Pere Arús
Source:
Scientia horticulturae 2022 v.293 pp. 110726
ISSN:
0304-4238
Subject:
chromosome mapping,   etc   ; DNA; backcrossing; color; cultivars; genomics; introgression; leaves; peaches; phenotype; progeny;     Show all 11 Subjects
Abstract:
... Based on detailed maps, DNA sequences and phenotypic data, there is a great deal of information on the genetics and genomics of ‘Earlygold’, a historical peach cultivar from the US. The F₂ between ‘Texas’ almond and ‘Earlygold’ peach (T × E) was used to construct the first saturated peach linkage map that later became the reference map for the Prunus genus. This population and the first backcross ...
DOI:
10.1016/j.scienta.2021.110726

9. Comparative genomics analysis and genome assembly integration with the recombination landscape contribute to Takifugu bimaculatus assembly refinement

Author:
Yue Shi; Baohua Chen; Shengnan Kong; Qingmin Zeng; Leibin Li; Bo Liu; Fei Pu; Peng Xu
Source:
Gene 2023 v.849 pp. 146910
ISSN:
0378-1119
Subject:
chromosome mapping,   etc   ; Takifugu; chromosomes; economic valuation; genes; genetic recombination; genome assembly; genomics;     Show all 8 Subjects
Abstract:
... Takifugu genus has been brought to the fore in scientific and practical research due to its compact genome, explosive speciation progress and economic value. Here we updated the chromosome-level genome of Takifugu bimaculatus by an ultra-high-density linkage map, a classic and accurate way of chromosome assembly. The map constituted a robust assembly frame, with 92.2% (372.77 Mb) of the draft geno ...
DOI:
10.1016/j.gene.2022.146910

10. Circular DNA in the human germline and its association with recombination

Author:
Rasmus Amund Henriksen; Piroon Jenjaroenpun; Ida Borup Sjøstrøm; Kristian Reveles Jensen; Iñigo Prada-Luengo; Thidathip Wongsurawat; Intawat Nookaew; Birgitte Regenberg
Source:
Molecular cell 2022 v.82 no.1 pp. 209-217.e7
ISSN:
1097-2765
Subject:
chromosome mapping,   etc   ; DNA fragmentation; circular DNA; genomics; humans; meiosis; microscopy; somatic cells; spermatozoa;     Show all 9 Subjects
Abstract:
... Extrachromosomal circular DNA (eccDNA) is common in somatic tissue, but its existence and effects in the human germline are unexplored. We used microscopy, long-read DNA sequencing, and new analytic methods to document thousands of eccDNAs from human sperm. EccDNAs derived from all genomic regions and mostly contained a single DNA fragment, although some consisted of multiple fragments. The genera ...
DOI:
10.1016/j.molcel.2021.11.027

11. Isolation and characterization of 34 SNP markers in Acipenser baerii

Author:
Quan Gong; Qingzhi Li; Jiahua Sun; Yu Xiao; Xutao Su; Guangxun Liu; Jun Du; Jue Lin
Source:
Conservation genetics resources 2022 v.14 no.1 pp. 11-14
ISSN:
1877-7260
Subject:
chromosome mapping,   etc   ; Acipenser baerii; conservation genetics; fish roe; gene frequency; heterozygosity; water pollution;     Show all 7 Subjects
Abstract:
... Acipenser baerii is one of the most important sources of caviar production. However, the population of the A. baerii is constantly being reduced in recent years due to dam construction, overfishing, and water pollution. Insufficient molecular markers have limited the effective conservation and management of this species; In the present study, we reported the isolation and characterization of 34 SN ...
DOI:
10.1007/s12686-021-01232-5

12. The design, validation, and utility of the “ZJU CottonSNP40K” liquid chip through genotyping by target sequencing

Author:
Zhanfeng Si; Shangkun Jin; Jiangyu Li; Zegang Han; Yiqian Li; Xiaonv Wu; Yunxia Ge; Lei Fang; Tianzhen Zhang; Yan Hu
Source:
Industrial crops and products 2022 v.188 pp. 115629
ISSN:
0926-6690
Subject:
chromosome mapping,   etc   ; cost effectiveness; cotton; genomics; genotype; genotyping; liquids; single nucleotide polymorphism arrays;     Show all 8 Subjects
Abstract:
... Genotyping platforms provide robust support for genomics, genetics, and molecular breeding. Given the economic importance of cotton, it is urgent to develop a cotton genotyping platform that features high throughput, precision, efficiency, and cost-effectiveness. Here we reported the development of a liquid SNP chip named “ZJU CottonSNP40K” through genotyping by target sequencing, along with its u ...
DOI:
10.1016/j.indcrop.2022.115629

13. Genetic mapping of simply inherited categorical traits, including anthocyanin accumulation profiles and fruit appearance, in eggplant (Solanum melongena)

Author:
Akio Ohyama; Hirotaka Yamaguchi; Koji Miyatake; Satomi Negoro; Tsukasa Nunome; Takeo Saito; Hiroyuki Fukuoka
Source:
Molecular biology reports 2022 v.49 no.10 pp. 9147-9157
ISSN:
0301-4851
Subject:
chromosome mapping,   etc   ; Solanum melongena; delphinidin; eggplants; fruits; genes; metabolism; molecular biology; myrtillin; tomatoes;     Show all 10 Subjects
Abstract:
... BACKGROUND: The appearance quality of the eggplant (Solanum melongena L.) fruit is an important trait that influences its commercial value. It is known that quality traits such as anthocyanin composition and fruit surface pattern are categorical and are inherited simply. However, research examples of gene mapping for the composition (anthocyanin accumulation profile) and the surface pattern in egg ...
DOI:
10.1007/s11033-022-07737-y

14. Identification and validation of QTLs for kernel number per spike and spike length in two founder genotypes of wheat

Author:
Xin Xu; Xiaojun Li; Dehua Zhang; Jishun Zhao; Xiaoling Jiang; Haili Sun; Zhengang Ru
Source:
BMC plant biology 2022 v.22 no.1 pp. 146
ISSN:
1471-2229
Subject:
chromosome mapping,   etc   ; alleles; cultivars; genotyping; inbred lines; marker-assisted selection; phenotype; seeds; wheat;     Show all 9 Subjects
Abstract:
... BACKGROUND: Kernel number per spike (KNS) and spike length (SL) are important spike-related traits in wheat variety improvement. Discovering genetic loci controlling these traits is necessary to elucidate the genetic basis of wheat yield traits and is very important for marker-assisted selection breeding. RESULTS: In the present study, we used a recombinant inbred line population with 248 lines de ...
DOI:
10.1186/s12870-022-03544-6

15. Construction of a genetic linkage map, QTLs mapping for low salinity and growth-related traits and identification of the candidate genes in Pacific white shrimp (Litopenaeus vannamei)

Author:
Bing Chen; Ping Zhong; Xiaopeng Wu; Kai Peng; Yuping Sun; Xiaoying Chen; Hongxia Zhao; Zhongneng Xu; Jinshang Liu; Huo Li; Chaozheng Li; Wen Huang
Source:
Aquaculture reports 2022 v.22 pp. 100978
ISSN:
2352-5134
Subject:
chromosome mapping,   etc   ; DNA; Litopenaeus vannamei; aquaculture; body weight; genomics; genotyping; quantitative traits; salinity; shrimp;     Show all 10 Subjects
Abstract:
... Low-salinity tolerance and growth are crucial economic traits of shrimp in areas with low-salinity water. In the current study, an F1 full-sib family of Pacific white shrimp (Litopenaeus vannamei) was obtained by the “semidirectional cross” method, and 2 parents and 146 progenies were genotyped using double-digest restriction site-associated DNA sequencing technology (ddRAD-Seq). A total of 3335 h ...
DOI:
10.1016/j.aqrep.2021.100978

16. QTL mapping, whole genome resequencing, and marker‐assisted selection provide basics of early flowering in pumpkin

Author:
Hafiz Muhammad Khalid Abbas; Yang Yang Zhou; He Xun Huang; Muhammad Tahir ul Qamar; Man Man Wang; Sen Lu; Congping Xu; Zhanshu Liu; Ting Quan Wu; Yu Juan Zhong
Source:
Plant breeding 2022 v.141 no.2 pp. 266-276
ISSN:
0179-9541
Subject:
chromosome mapping,   etc   ; females; genes; loci; males; marker-assisted selection; pumpkins; quantitative traits; sequence analysis;     Show all 9 Subjects
Abstract:
... Finding the quantitative trait loci (QTLs) and uncovering the genes controlling early flowering in pumpkin are the basic needs to select appropriate varieties for cultivation. Two QTLs related to first female flowering node (FFFN) and four QTLs related to first male flowering node (FMFN) were detected based on high‐density genetic map of pumpkin. Based on annotation information, two candidate gene ...
DOI:
10.1111/pbr.12996

17. Genome-wide identification of quantitative trait loci for morpho-agronomic and yield-related traits in foxtail millet (Setaria italica) across multi-environments

Author:
Tianpeng Liu; Jihong He; Kongjun Dong; Xuewen Wang; Lei Zhang; Ruiyu Ren; Sha Huang; Xiaoting Sun; Wanxiang Pan; Wenwen Wang; Peng Yang; Tianyu Yang; Zhengsheng Zhang
Source:
Molecular genetics and genomics 2022 v.297 no.3 pp. 873-888
ISSN:
1617-4615
Subject:
chromosome mapping,   etc   ; Setaria italica; dissection; genomics; models; panicles; phenotypic variation; plant height; quantitative traits;     Show all 9 Subjects
Abstract:
... Foxtail millet (Setaria italica) is an ideal model of genetic system for functional genomics of the Panicoideae crop. Identification of QTL responsible for morpho-agronomic and yield-related traits facilitates dissection of genetic control and breeding in cereal crops. Here, based on a Yugu1 × Longgu7 RIL population and genome-wide resequencing data, an updated linkage map harboring 2297 bin and 7 ...
DOI:
10.1007/s00438-022-01894-2

18. High-density genetic map and quantitative trait loci map of fruit-related traits in wax gourd (Benincasa hispida)

Author:
Liwen Su; Jiquan Gou; Haixuan Lv; Zhikui Cheng; Lianlian Ma; Xiaochun Huang; Wenting Wu; Wenjin Yu; Peng Wang; Zhengguo Liu
Source:
Euphytica 2022 v.218 no.8 pp. 117
ISSN:
0014-2336
Subject:
chromosome mapping,   etc   ; Benincasa hispida; chromosomes; color; fruits; genotyping; horticultural crops; phenotypic variation; quantitative traits;     Show all 9 Subjects
Abstract:
... Wax gourd (Benincasa hispida [Thunb] Cogn.) is an important horticultural crop in the Cucurbitaceae family that has high nutritive and medicinal value. We analysed quantitative trait loci (QTLs) related to the fruit-related traits of wax gourd by constructing a high-density genetic map through whole-genome resequencing. We obtained an F₂ population of 195 individuals by crossing two inbred wax gou ...
DOI:
10.1007/s10681-022-03074-0

19. Molecular mapping for fruit-related traits, and joint identification of candidate genes and selective sweeps for seed size in melon

Author:
Hong Zhang; Xuejun Zhang; Meihua Li; Yong Yang; Zhiqiang Li; Yuhui Xu; Haojie Wang; Dengming Wang; Yongbing Zhang; Huaisong Wang; Qiushi Fu; Jing Zheng; Hongping Yi
Source:
Genomics 2022 v.114 no.2 pp. 110306
ISSN:
0888-7543
Subject:
chromosome mapping,   etc   ; Arabidopsis; fruits; genomics; genotyping; melons; rice; seed size; sequence analysis; vegetable crops;     Show all 10 Subjects
Abstract:
... Melon is a popular fruit vegetable crop worldwide with diverse morphological variation. We report a high-density genetic map of melon and nine major QTLs with physical region ranging from 43.47 kb to 1.89 Mb. Importantly, two seed-related trait QTLs were repeatedly detected in two environments, and the mapping region was narrowed to 522 kb according to a regional linkage analysis. A total of 40 an ...
DOI:
10.1016/j.ygeno.2022.110306

20. QTL identification, fine mapping, and marker development for breeding peanut (Arachis hypogaea L.) resistant to bacterial wilt

Author:
Feiyan Qi; Ziqi Sun; Hua Liu; Zheng Zheng; Li Qin; Lei Shi; Qingzheng Chen; Haidong Liu; Xiufang Lin; Lijuan Miao; Mengdi Tian; Xiao Wang; Bingyan Huang; Wenzhao Dong; Xinyou Zhang
Source:
Theoretical and applied genetics 2022 v.135 no.4 pp. 1319-1330
ISSN:
0040-5752
Subject:
chromosome mapping,   etc   ; Arachis hypogaea; DNA; Ralstonia solanacearum; bacterial wilt; disease resistance; germplasm; peanuts; China;     Show all 9 Subjects
Abstract:
... KEY MESSAGE: A major QTL, qBWA12, was fine mapped to a 216.68 kb physical region, and A12.4097252 was identified as a useful KASP marker for breeding peanut varieties resistant to bacterial wilt. Bacterial wilt, caused by Ralstonia solanacearum, is a major disease detrimental to peanut production in China. Breeding disease-resistant peanut varieties is the most economical and effective way to prev ...
DOI:
10.1007/s00122-022-04033-y