Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L.

Gailing, Oliver; Staton, Margaret; Lane, Thomas; Schlarbaum, Scott E.; Nipper, Rick; Owusu, Sandra A.; Carlson, John E.

doi:10.1007/s11105-016-1012-0

Cited by 10 publications

(10 citation statements)

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“…However, if distorted markers are ignored, map coverage may decrease and some important information in the real data analysis of QTL mapping may lose [123, 124]. Several genetic linkage maps using second-generation markers contain some skewed markers [118, 125, 126]. In the present study, the genetic linkage map contained 20 skewed markers, of which 14 markers formed six SDRs, and the coverage was 93.71%, which was higher than that (88.1%) of P. haitanensis without skewed markers [23].…”

Section: Discussionmentioning

confidence: 99%

Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades

Huang

Yan

2018

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17 Pyropia yezoensis is an important economic seaweed, to construct a genetic linkage map 18 and analyze the quantitative trait loci (QTLs) of blades, a doubled haploid (DH) 19 population containing 148 DH strains established from the intraspecific hybridization 20 between two strains with different colors was used in the present study and genotyped 21 using 79 pairs of polymorphic sequence-related amplified polymorphism (SRAP) 22 markers labeled with 5'-HEX and capillary electrophoresis. A chi-square test for 23 significance of deviations from the expected ratio (1:1) on the loci which were 24 polymorphic between parents and segregated in mapping population identified 301 loci 25 with normal segregation (P ≥ 0.01) and 96 loci (24.18%) with low-level skewed 26 segregation (0.001 ≤ P < 0.01). The map was constructed using JoinMap software after a 27 total of 92 loci were assembled into three linkage groups. The map spanned 557.36 cM 28 covering 93.71% of the estimated genome, with a mean interlocus space of 6.23 cM.29 Kolmogorov-Smirnov test (α=5%) of the marker positions along each LG showed a 30 uniform distribution. After that, 10 QTLs associated with five economic traits of blades 31 were detected, among which one QTL was for length, one for width, two for fresh 32 weight, two for specific growth rate of length and four for specific growth rate of fresh 33 weight. These QTLs could explain 2.29-7.87% of the trait variations, indicating that 34 their effects were all minor. The results will serve as a framework for future marker-35 assisted breeding in P. yezoensis. 36 37 Keywords: Economic trait; genetic linkage map; Pyropia yezoensis; quantitative trait 38 locus; SRAP 39 40 Introduction 41 Pyropia yezoensis is a marine red alga with high nutritional values and is one of the 42 most important maricultural crops across the world, mainly in Japan, Korea and China 43 [1]. During the cultivation of P. yezoensis, hundreds of tons of nutrients (nitrogen and 44 phosphorus) are removed by blade harvest from the eutrophic seawaters every year [2]. 45 However, some problems such as germplasm degeneration, frequent diseases and bad 46 harvests [3-5] have arisen under the influence of global warming [6]. Therefore, new 47 varieties with higher yield, stronger resistant to abiotic stress and greater ecological 48 adaptability were urgently needed for the stable development of Pyropia industry. 49 50 The traditional breeding methods of P. yezoensis are based on either observed variations 51 by selecting blades with induced variants [3, 7, 8], or controlled crosses by selecting 52 blades presenting recombination of desirable genes from different parents [9-11]. 53 However, traditional breeding is usually time-consuming and less efficient [12], and has 54 a limited ability to breed complex characters [13]. Fortunately, progress in molecular 55 genetics has enabled plant breeders the direct selection of genotypes, thereby accelerates 56 crop improvement [14]. Molecular marker-assisted selection (MAS) has become the 57 main d...

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Section: Discussionmentioning

confidence: 99%

Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades

Huang

Yan

2018

Preprint

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“…Additionally, genetic characterization at these markers can be performed in populations from contrasting environments or along environmental gradients to test for selective neutrality of markers. Finally, a framework genetic linkage map was generated in honeylocust using restriction site associated DNA sequencing (RAD-seq) derived SNPs (Gailing et al 2017). The map consists of 178 SNPs distributed across the 14 haploid chromosomes of the honeylocust genome.…”

Section: Discussionmentioning

confidence: 99%

“…Honeylocust is also a popular fast-growing landscape plant and is suitable for planting in disturbed environments (Schnabel & Wendel 1998, Preston & Braham 2002. It is a member of the subfamily Caesalpinioideae, for which only a limited number of markers and other genomic resources are available (La Malfa et al 2014, Gailing et al 2017. The transfer of genic microsatellites (Expressed Sequence Tag-Simple Sequence Repeats (EST-SSRs)) developed for the related species Ceratonia siliqua L. (La Malfa et al 2014) to honeylocust was not successful (Owusu et al 2013).…”

Section: Introductionmentioning

confidence: 99%

“…As part of the Hardwood Genomics project (http://www.hardwoodgenomics.org/) we are developing genome/transcriptome resources and genetic linkage maps in eastern North American hardwood species from different taxonomic orders. For honeylocust, we have developed genomic SSRs (Owusu et al 2013) for genetic variation and gene flow analyses (Owusu et al 2016) and a framework genetic linkage map for Quantitative Trait Locus (QTL) and comparative mapping based on restriction site associated sequencing (RAD-seq) markers (Gailing et al 2017). …”

Section: Introductionmentioning

confidence: 99%

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Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

et al. 2017

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Abstract. Twenty new polymorphic genic SSRs (EST-SSRs) and 13 genomic SSRs were developed in honeylocust (Gleditsia triacanthos) using Illumina transcriptome and low-coverage genome sequencing. A diversity panel of 40 honeylocust samples covering large parts of the species distribution range was characterized. As expected the level of genetic variation was lower in EST-SSRs than for non-genic genomic SSRs. This is the first report of ESTSSRs for honeylocust. All markers are polymorphic and produce clear single locus amplification products and can be used for genetic diversity and gene flow analyses. The transcriptome sequencing data provide a rich resource for new marker development.

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“…Recently, transcriptome sequencing is essential for functional gene annotation, novel gene discovery, differential gene expression, and molecular marker research [30][31][32]. RNA sequencing (RNA-seq) enables the study of gene expression at the transcriptome level and identifies genes involved in plant-specific biological processes [33][34][35]. So far, with the introduction of a new generation of RNAseq, transcriptome sequencing technology has been used for identify low temperature stress response genes in Ipomoea batatas [36], Brassica napus [37], Populus tomentosa [38], Capsicum annuum [39], and Magnolia wufengensis [40].…”

Section: Introductionmentioning

confidence: 99%

Different Genes Express Analysis of root crown of alfalfa under low temperature stress

Wang

Jin

Meng

et al. 2019

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Background: Alfalfa ( Medicago sativa ) is a perennial forage crop widely cultivated in northern China. The root crown of alfalfa is an important storage organ in the process of wintering, and it is closely related to the winter hardiness of alfalfa. At present, the specific molecular mechanism of response to winter hardiness in alfalfa root crown is unclear. The transcriptome database created by RNA sequencing (RNA-seq) is widely used to identify the critical genes related to winter hardiness. Results: The transcriptomes of alfalfa varieties, such as “Lomgmu 806” (with high winter survival rate) and “Sardi” (with low winter survival rate) have been sequenced in the study. Among the identified 57,712 unigenes, 2,299 differentially expressed genes (DEGs) were up-regulated, and 2,143 unigenes were down-regulated in the Lomgmu 806 vs Sardi root crown. The KEGG pathway annotations showed that 1,159 unigenes were mainly annotated to 116 pathways. Seven DEGs belonging to “plant hormone signaling transduction”, “peroxidase” pathway and transcription factors family (MYB, B3, AP2/ERF, WRKY) genes involved in alfalfa winter hardiness. Among them, the expression patterns of seven DEGs were verified by real-time quantitative PCR (RT-qPCR) analyses, which verified the reliable results of transcriptome sequencing analyses. Conclusions: RNA-Seq was used to discover genes associated with the wintering differences between alfalfa varieties. The transcriptome data showed that the gene regulation response of alfalfa to low temperature stress, which provides a valuable resource for further identification and functional analysis of candidate genes for winter hardiness of alfalfa. In addition, these data provide references for future study of genetic breeding and winter hardiness in alfalfa.

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Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L.

Cited by 10 publications

References 55 publications

Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades

Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades

Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

Different Genes Express Analysis of root crown of alfalfa under low temperature stress

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