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Analysis of rbcL (Ribulose-1,5-Biphosphate carboxylase) gene sequences of identified noxious weed species (Poaceae)

Christian Joseph N. Ong, Mariane Lou C. Obligar, Thelma DC. Arrieta, Oliver R. Alaijos

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J. Bio. Env. Sci.19(4), 36-46, October 2021

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Abstract

Noxious weed species usually ranks as a first or second problem in weed management, reduce farm productivity and increase weed control costs. Traditionally, identification of noxious grasses has generally relied on the morphological examination of grass floral material. Morphologically, about five species of grass weeds were identified and one species was identified only by genus level. These include Eleusine indica (L.) Gaertn., Echinochloa crus-galli (L.) P. Beauv., Echinochloa stagnina (Retz.) P. Beauv., Ischaemum rugosum Salisb. Var. distachyum (Cav.) Merr., Leptochloa chinensis (L.) Nees. and Echinochloa sp., respectively. DNA Barcoding may provide alternative means to identify noxious weed species. The utilization of genomic techniques depicted the rbcL gene in these plants, and have yielded a good amplification ranging from 500-850 base pairs (bp) in size. The BLASTN search results accumulated 95 – 98% maximum gene identity from the significant hits of specific species related from their rbcL gene sequences. The 9 rbcL gene sequences except Sample ID BS1 was input in MEGA X and were aligned and computed using Kimura- 2 Parameter (K2P) method. Single Nucleotide Polymorphisms (SNPs) variation analyses were used and identified 27 SNPs variant size among 9 rbcL gene sequences. Moreover, the 9 rbcL gene sequences were submitted and published to GenBank through BankIt, and have provided accession numbers. The molecular and phylogenetic relationships of rbcL gene in noxious weed species that were described and evaluated in this study may serve as baseline data for weed barcoding studies and enhancing weed management in rice cropping systems.

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Analysis of rbcL (Ribulose-1,5-Biphosphate carboxylase) gene sequences of identified noxious weed species (Poaceae)

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