Characteristics and analysis of simple sequence repeats in the cotton genome based on a linkage map constructed from a BC1 population between Gossypium hirsutum and G. barbadense

Genome ◽  
2008 ◽  
Vol 51 (7) ◽  
pp. 534-546 ◽  
Author(s):  
Yanxin Zhang ◽  
Zhongxu Lin ◽  
Qizhong Xia ◽  
Mingju Zhang ◽  
Xianlong Zhang
Keyword(s):  
Gossypium Hirsutum ◽  
Linkage Map ◽  
Expressed Sequence Tag ◽  
Average Distance ◽  
Dinucleotide Repeats ◽  
Genome Wide ◽  
Size Type ◽  
Simple Sequence ◽  
Mapping Populations ◽  
Allotetraploid Cotton

In the past decade, several molecular maps of cotton have been constructed using diverse DNA molecular markers and mapping populations. In this study, an interspecific linkage map of allotetraploid cotton was developed using a BC1 population ((Gossypium hirsutum × G. barbadense) × G. hirsutum). This map was genome-wide and was based entirely on simple sequence repeat (SSR) markers. Forty-four linkage groups were assigned to 26 chromosomes, with 917 loci spanning 5452.2 cM of the genome. The average distance between loci was 5.9 cM, providing uniform coverage of the A subgenome and D subgenome. Characteristics of this map were analyzed in detail, including the distributions of genomic SSRs, expressed sequence tag (EST)-SSRs, and distorted markers. Furthermore, the relationships between motif characteristics (size, type, length) and the level of polymorphism in EST-SSRs were also surveyed. The results showed that tetranucleotide and dinucleotide repeats had similar levels of polymorphism, and ACAT, AC, and ACT repeats had the highest polymorphism rates. Loci with lengths of 27 bp, 33 bp, and 24 bp were more likely to be polymorphic. This work will provide information to assist in designing future EST-SSRs.

scholarly journals Identification of Expressed Sequence Tag-simple Sequence Repeat Markers from the De Novo Transcriptome Sequence of Red Raspberry (Rubus idaeus L.)

HortScience ◽  
2017 ◽  
Vol 52 (4) ◽  
pp. 554-559
Author(s):  
Jianfeng Liu ◽  
Bowen Yang ◽  
Yuetong Ming ◽  
Yuchu Zhang ◽  
Yunqing Cheng
Keyword(s):  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Rubus Idaeus ◽  
Group Method ◽  
Sequence Repeat ◽  
Red Raspberry ◽  
De Novo Transcriptome ◽  
Dinucleotide Repeats ◽  
Simple Sequence

Rubus idaeus has remarkable economic and cultural value. Developing efficient simple sequence repeat (SSR) markers is necessary for the molecular breeding of red raspberry. In this study, SSR mining was performed using the de novo transcriptome sequence of R. idaeus. In total, 14,210 SSR sequences were identified from 11,158 SSR-containing unigenes. In all the SSR sequences, mononucleotide, dinucleotide, and trinucleotide repeats were the most common, and their number and percentage were 1323 (9.31%), 6752 (47.52%), and 4897 (34.46%), respectively. Of the mononucleotide and dinucleotide repeats, A/T, AG/CT, AT/AT, and AC/GT were more abundant and accounted for 9.09%, 37.82%, 6.51%, and 3.14% of the total repeat number, respectively. In the trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide repeats, the nucleotide (NT) patterns AAG/CTT, AAAG/CTTT, AAAAG/CTTTT, and AAGAGG/CCTCTT were the most frequent, and accounted for 14.11%, 0.38%, 0.57%, and 0.23% of the total SSRs, respectively. Of the 480 SSR-containing unigenes with gene ontology (GO) annotation, the classification results showed that they were mainly involved in binding, catalytic, and transporter molecular functions. Most of the 3441 SSR-containing unigenes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation were involved in the following top five pathways: metabolic, RNA transport, spliceosome, protein processing in the endoplasmic reticulum, and mRNA surveillance. Thirty pairs of primers derived from the red raspberry transcriptome were randomly selected to assess their polymorphism by using 15 red raspberry germplasms, in which the polymorphism information content (PIC) values ranged from 0.50 to 0.86, with a mean of 0.73, thereby indicating a high level of polymorphism. The unweighted pair group method with arithmetic mean clustering results indicated that the thirty pairs of primers could precisely distinguish the germplasms. This study reveals the SSR distribution characteristics of red raspberry and provides a scientific basis for further genetic diversity studies and genetic linkage map construction for this species.

scholarly journals Genetic and Physical Mapping of Genic Microsatellites in Barley (Hordeum vulgare L.)

2011 ◽  
Vol 41 (No. 4) ◽  
pp. 153-159
Author(s):  
R.K. Varshney ◽  
U. Hähnel ◽  
T. Thiel ◽  
N. Stein ◽  
L. Altschmied ◽  
...  
Keyword(s):  
Large Scale ◽  
Expressed Sequence Tag ◽  
Sequence Data ◽  
Bac Library ◽  
Linkage Groups ◽  
Hordeum Vulgare L ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Mapping Populations ◽  
Genic Microsatellites

Due to the availability of sequence data from large-scale EST (expressed sequence tag) projects, it has become feasible to develop microsatellite or simple sequence repeat (SSR) markers from genes. A set of 111 090 barley ESTs (corresponding to 55.9 Mb of sequence) was employed for the identification of microsatellites with the help of a PERL5 script called MISA. As a result, a total of 9 564 microsatellites were identified in 8 766 ESTs (SSR-ESTs). Cluster analysis revealed the presence of 2 823 non-redundant SSR-ESTs in this set. From these 754 primer pairs were designed and analysed in a set of seven genotypes including the parents of three mapping populations. Finally, 185 microsatellite (EST-SSRs) loci were placed onto the barley genetic map. These markers show a uniform distribution on all the linkage groups ranging from 21 markers (on 7H) to 35 markers (3H). The polymorphism information content (PIC) for the developed markers ranged from 0.24 to 0.78 with an average of 0.48. For the assignment of these markers to BAC clones, a PCR-based strategy was established to screen the “Morex”-BAC library. By using this strategy BAC addresses were obtained for a total of 127 mapped EST-SSRs, which may provide at least two markers located on a single BAC. This observation is indicative of an uneven distribution of genes and may lead to the identification of gene-rich regions in the barley genome.  

scholarly journals An Extended Linkage Map for Watermelon Based on SRAP, AFLP, SSR, ISSR, and RAPD Markers

2006 ◽  
Vol 131 (3) ◽  
pp. 393-402 ◽  
Author(s):  
A. Levi ◽  
C.E. Thomas ◽  
T. Trebitsh ◽  
A. Salman ◽  
J. King ◽  
...  
Keyword(s):  
Linkage Map ◽  
Simple Sequence Repeat ◽  
Citrullus Lanatus ◽  
Average Distance ◽  
Acc Synthase ◽  
Segregation Ratio ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Simple Sequence

Seventy-one amplified fragment length polymorphism (AFLP), 93 sequence related amplified polymorphism (SRAP), and 14 simple sequence repeat (SSR) markers were used to extend an initial genetic linkage map for watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai]. The initial map was based on 151 randomly amplified polymorphic DNA (RAPD) and 30 and inter-simple sequence repeat (ISSR) markers. A testcross population previously used for mapping of RAPD and ISSR markers was used in this study: {plant accession Griffin 14113 [C. lanatus var. citroide (L.H. Bailey) Mansf.] × the watermelon cultivar New Hampshire Midget (C. lanatus var. lanatus)} × PI 386015 [C. colocynthis (L.) Schrad.]. The linkage map contains 360 DNA markers distributed on 19 linkage groups, and covers a genetic distance of 1976 cM with an average distance of 5.8 cM between two markers. A genomic DNA clone representing 1-amino-cyclopropane-1-carboxylic acid (ACC-) synthase gene, involved in ethylene biosynthesis, was also mapped. As in previous mapping studies for watermelon, a large number of AFLP and SRAP markers were skewed away from the 1:1 segregation ratio, and had to be excluded from the final mapping analysis. The stringent mapping criteria (JoinMap 3.0 mapping program) produced linkage groups with marker order consistent with those reported in previous mapping study for watermelon.

Constructing a genetic linkage map and mapping quantitative trait loci for skeletal traits in Japanese flounder

Biologia ◽  
2013 ◽  
Vol 68 (6) ◽  
Author(s):  
Yi Liu ◽  
Yongxin Liu ◽  
Yingjie Liu ◽  
Xiaoyan Zhang ◽  
Fei Si ◽  
...  
Keyword(s):  
Linkage Map ◽  
Quantitative Trait ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Expressed Sequence Tag ◽  
Average Distance ◽  
Doubled Haploids ◽  
Japanese Flounder ◽  
Type Ii ◽  
Linkage Groups

AbstractA genetic linkage map of Japanese flounder was constructed using 165 doubled haploids (DHs) derived from a single female. A total of 574 genomic microsatellites (type II SSRs) and expressed sequence tag (EST)-derived markers (EST-SSRs) were mapped to 24 linkage groups. The length of linkage map was estimated as 1270.9 centiMorgans (cM), with an average distance between markers of 2.2 cM. The EST-SSRs were used together with type II SSR markers to construct the Japanese flounder genetic linkage map which will facilitate identify quantitative trait locus (QTL) controlling important economic traits in Japanese flounder. Thus, twelve skeletal traits at 2 years of age were measured for all DHs. Forty-one QTLs were detected on 14 linkage groups and totally account for a small proportion of phenotypic variation (4.5 to 17.3%). Most of QTLs detected distribute on linkage groups 5 (9 QTLs), 8 (9 QTLs), 9 (5 QTLs) and 20 (4 QTLs), in which, some QTLs perform the pleiotropy.

scholarly journals Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton (Gossypium hirsutum L.)

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Lingling DOU ◽  
Limin LV ◽  
Yangyang KANG ◽  
Ruijie TIAN ◽  
Deqing HUANG ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Segmental Duplication ◽  
Gene Expression Pattern ◽  
Cell Development ◽  
Fiber Cell ◽  
Fiber Cells ◽  
Genome Wide ◽  
Duplication Events ◽  
Signaling Receptors

Abstract Background Calmodulin (CaM) is one of the most important Ca2+ signaling receptors because it regulates diverse physiological and biochemical reactions in plants. CaM functions by interacting with CaM-binding proteins (CaMBPs) to modulate Ca2+ signaling. IQ domain (IQD) proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites. Results In this study, we identified 102 GhIQD genes in the Gossypium hirsutum L. genome. The GhIQD gene family was classified into four clusters (I, II, III, and IV), and we then mapped the GhIQD genes to the G. hirsutum L. chromosomes. Moreover, we found that 100 of the 102 GhIQD genes resulted from segmental duplication events, indicating that segmental duplication is the main force driving GhIQD gene expansion. Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells, suggesting that GhIQD genes may contribute to fiber cell development in cotton. In addition, we found that 20 selected GhIQD genes were highly expressed in various tissues. Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes. Conclusions Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA. Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes, as well as clues to breed better cotton varieties in the future.

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