DNA base analysis: An effective tool to resolve taxonomic uncertainty and establish phylogenetic relationship in cryptic genotypes of Pyrus (pear), Rosaceae

• Published in: South African journal of botany 2023-11, Vol.162, p.901-912
• Main Authors: Akhtar, Muhammad Saeed, Khan, Shahid Ullah, Saleh, Ebraheem Abdu Musad, Muhammad, Said, Islam, Mohammad, Zaman, Umber, ur Rehman, Khalil, Nawab, Gul, Akhtar, Muhammad Naveed, Alhakamy, Nabil A., Rasha Ibrahim, M.K., Abdelrahman, Ehab A.
• Format: Article
• Language: English
• Subjects: agarose; bioinformatics; cross pollination; DNA; family; gels; genetic variation; genotype; genus; health care; heterogeneity; horticulture; Malus; molecular analysis; nucleobases; Pakistan; pears; phylogeny; Pyrus (pear) genotypes; Pyrus pyrifolia; species; uncertainty
• ISSN: 0254-6299; 1727-9321
• DOI: 10.1016/j.sajb.2023.10.013

In the current study, a total of 16 Pyrus (pear) were collected from the Biayari Valley, Allai, KP, Pakistan. A good quality gDNA was extracted, target region of DNA of each genotype was amplified through PCR, amplified region of DNA was extracted from agarose gel and was sequenced. Among 16 sequences, good quality 09 query sequences were analyzed through different bioinformatics tools and techniques for establishment of phylogenetic tree. Molecular analysis showed that the query genotype-B1"Tora tangai" possess 86% identity and 100% query cover with P. sinkiangensis, P. communis, and P. pyrifolia, while the query genotype-B2 “Kado batang” showed 83 % identity and 98 % query cover with P. communis, P. ussuriensis, and P. pyrifolia. Similarly, the query genotype-B6 “Shakar batang” possess 86% identity and 69% query cover with P. Malus rockii, Malus rocki, P. pyrifolia, and P. communis. The query genotype-B7 “kado batang” showed 92% identity and 13% query cover with; P. sinkiangensis, P. pyrifolia, P. communis, P. domestica The query genotypeB9 "Mamosai" revealed 98% identity and 3% query cover with genotype P. pyrifolia, Malus rokii, P. ussuriensis, and P. sinkiangensis. Similarly, BLAST search result showed that query genotype-C1 “Kado batang” possess 95% identity and 91% query cover with P. calleryana, P. pyrifolia, P. pyrifolia, P. pyrifolia, and P. pyraster. Initial search result revealed that the query genotype-C4 “Nashpati” has 42% query cover and 95% identity with; P. dimorphophylla, P. dimorphophylla, P. pashia, P. pashia P. ussuriensis. and similarly, genotype-D1 “Nashpati” showed 93% identity and 9% query cover with, Pyrus pyrifolia and Pyrus x domestica. Over all, BLAST search result showed that all the query genotypes possess maximum identity and query cover with different species of the genus Pyrus (pear), family Rosaceae. Further, phylogenetic tree showed that the query genotypes B1, B2, B6, B7, B8, C1, C2 and C4 fall independently due to its slight genetic variation, an indication for development of sub-species and new varieties. This genetic variation is due cross pollination and their availability in the wild form decades. These finding promote horticulture especially in development of new varieties in pear. Extraction and PCR amplification of DNA [Display omitted] •DNA Barcoding of economically important Plant and molecular Identification.•Genotyping by sequencing approach for Plant biosystematics.•Phylogenetic analyses of Pyrus within its