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DNA Barcoding in Selected Species and Subspecies of Rye (Secale) Using Three Chloroplast Loci (matK, rbcL, trnH-psbA)

Lidia SKUZA, Izabela SZUĆKO, Ewa FILIP, Anastazja ADAMCZYK

Abstract


DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Secale. In this study the plant material consisted of 10 cultivated and non-cultivated species and subspecies of rye genus. Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions. Universal primers were used, and sequenced products were analyzed using Neighbor Joining and the Maximum Likelihood in the MEGA 7.1 program. We did not observe high variability in nucleotide sequences within the matK and rbcL regions. Only 2.2% of the sequences showed polymorphism in the rbcL region, while 6.5% in the matK region. The most variable trnH-psbA (15.6%) intergenic region was the most useful for rye barcoding. Individual application of the studied regions did not provide the expected results. None of the regions used in the study allowed the division of rye species and subspecies according to the adopted classification of the genus Secale. The results confirm that the use of matK and rbcL is insufficient for DNA barcoding in rye species, and better discrimination within the genus Secale can be obtained only in combination with the non-coding trnH-psbA sequence. Our results also indicate the necessity of using a different region. All of the new sequences have been deposited in Genbank.

 

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In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 1, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI number will become active after the article will be included in the complete issue.


Keywords


barcoding DNA; rye; cpDNA; intergenic spacer

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References


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DOI: http://dx.doi.org/10.15835/nbha47111248

June 1, 2018: Notulae Botanicae Horti Agrobotanici Cluj-Napoca in Scopus – Elsevier CiteScore 2017=0.78, Horticulture; Agronomy and Crop Science; Plant Science


 
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