The development of 204 novel EST-SSRs and their use for genetic diversity analyses in cultivated alfalfa

Zhou, Qiang; Chen, Tianlong; Wang, Yanrong; Liu, Wenxian

doi:10.1016/j.bse.2014.08.023

Cited by 26 publications

(20 citation statements)

References 21 publications

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“…To date, many SSRs have been developed in many plants through Illumina sequencing; these plants include alfalfa 13 14 , Vicia sativa 15 , and Indian sesame 16 . However, in the genus Elymus , the applications of SSRs have only been presented in a few species, including E. alaskanus 5 , E. caninus 17 , E. trachycaulus 18 , and E .…”

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confidence: 99%

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

Zhou

Luo

et al. 2016

Sci Rep

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Siberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance. However, the transcriptomic and genomic information on this species is very limited, which hinders genetic and breeding studies. In the present study, 76,686,804 clean reads were generated from 11 different tissue samples of E. sibiricus by Illumina paired-end sequencing, and the reads were deposited into the NCBI SRA database (SRX574376). A total of 8,769 EST-SSRs were identified from 94,458 unigene sequences, which were obtained by de novo assembly. Moreover, 1,078 primer pairs were successfully designed, and 500 pairs were randomly selected to assess polymorphisms in 15 E. sibiricus accessions. A total of 112 primer pairs were polymorphic, and the polymorphism information content (PIC) values ranged from 0.39 to 0.81, indicating a high level of informativeness. Furthermore, these 112 polymorphic primer pairs were used to evaluate the transferability to 13 other related species, and 55 EST-SSR markers were found to be polymorphic among these 13 Elymus species. This study collected the global sequence data for E. sibiricus, and the newly developed markers will prove valuable in facilitating genetic diversity in E. sibiricus and related Elymus species.

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confidence: 99%

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

Zhou

Luo

et al. 2016

Sci Rep

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“…Additionally, alfalfa is different from A. thaliana and other model plants, and it is an obligate outcrossing, autotetraploid (2n = 4x = 32) plant. Thus, there is genetic diversity between individual plants of alfalfa (Liu et al, 2013;Zhou et al, 2014), which may be another important reason for inconsistencies between RNAseq and RT-qPCR data. A previous study reported that ABRE is the major cis-element for ABA-responsive gene expression (Yamaguchi- Shinozaki & Shinozaki, 2006).…”

Section: Discussionmentioning

confidence: 99%

Peer Review #1 of "MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses (v0.1)"

2019

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Background. Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. Its survival and production are often hampered by environmental changes. However, there are few studies on stress-resistance genes in alfalfa because of its incomplete genomic information and rare expression profile data. The MYB proteins are characterized by a highly conserved DNA-binding domain, which is large, functionally diverse, and represented in all eukaryotes. The role of MYB proteins in plant development is essential; they function in diverse biological processes, including stress and defense responses, and seed and floral development. Studies on the MYB gene family have been reported in several species, but they have not been comprehensively analyzed in alfalfa. Methods. To identify more comprehensive MYB transcription factor family genes, the sequences of 168 Arabidopsis thaliana, 430 Glycine max, 185 Medicago truncatula, and 130 Oryza sativa MYB proteins were downloaded from the Plant Transcription Factor Database. These sequences were used as queries in a BLAST search against the Medicago sativa proteome sequences provided by the Noble Research Institute. Results. In the present study, a total of 265 MsMYB proteins were obtained, including 50 R1-MYB, 186 R2R3-MYB, 26 R1R2R3-MYB, and three atypical-MYB proteins. These predicted MsMYB proteins were divided into 12 subgroups by phylogenetic analysis, and gene ontology (GO) analysis indicated that most of the MsMYB genes are involved in various biological processes. The expression profiles and quantitative real-time PCR analysis indicated that some MsMYB genes might play a crucial role in the response to abiotic stresses. Additionally, a total of 170 and 914 predicted protein-protein and protein-DNA interactions were obtained, respectively. The interactions between MsMYB043 and MSAD320162, MsMYB253 and MSAD320162, and MsMYB253 and MSAD308489 were confirmed by a yeast two-hybrid system. This work provides information on the MYB family in alfalfa that was previously lacking and might promotes the cultivation of stress-resistant alfalfa.

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“…The distribution of H E values revealed the presence of high heterozygosity within Jerusalem artichoke populations, and showed that 67% of the markers are within the range 0.5 to 0.8 (Figure 2). This might contribute to the auto-tetraploidy and cross-pollination observed for this species (Zhou et al, 2014). Ta = annealing temperature.…”

Section: Primer Development and Validationmentioning

confidence: 94%

Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.)

Mornkham¹,

Wangsomnuk²,

Mo³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Jerusalem artichoke (Helianthus tuberosus L.) is a perennial tuberous plant and a traditional inulin-rich crop in Thailand. It has become the most important source of inulin and has great potential for use in chemical and food industries. In this study, expressed sequence tag (EST)-based simple sequence repeat (SSR) markers were developed from 40,362 Jerusalem artichoke ESTs retrieved from the NCBI database. Among 23,691 non-redundant identified ESTs, 1949 SSR motifs harboring 2 to 6 nucleotides with varied repeat motifs were discovered from 1676 assembled sequences. Seventy-nine primer pairs were generated from EST sequences harboring SSR motifs. Our results show that 43 primers are polymorphic for the six studied populations, while the remaining 36 were either monomorphic or failed to amplify. These 43 SSR loci exhibited a high level of genetic diversity among populations, with allele numbers varying from 2 to 7, with an average of 3.95 alleles per loci. Heterozygosity ranged from 0.096 to 0.774, with an average of 0.536; polymorphic index content ranged from 0.096 to 0.854, with an average of 0.568. Principal component analysis and neighbor-joining analysis revealed that the six populations could be divided into six clusters. Our results indicate that these newly characterized EST-SSR markers may be useful in the exploration of genetic diversity and range expansion of the Jerusalem artichoke, and in cross-species application for the genus Helianthus.

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The development of 204 novel EST-SSRs and their use for genetic diversity analyses in cultivated alfalfa

Cited by 26 publications

References 21 publications

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

Peer Review #1 of "MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses (v0.1)"

Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.)

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