Determination of Morphological and Genetic Diversity of ALS (Acetolactate Synthase)- Herbicide-Resistant Echinochloa oryzoides Biotypes in Rice

Abstract

This work aimed to evaluate the genetic and morphological diversity of 62 biotypes of Echinochloa oryzoides (Ard.) Fritsch.(early watergrass) that are resistant to ALS-inhibitor herbicides (bispyribac-sodium and penoxsulam), using the single sequence repeat (SSR) marker system. To determine the morphological diversity, the weed was grown (five seeds from each population) under screenhouse conditions and morphological characteristics were recorded. Parameter values subjected to a hierarchical clustering analysis showed significant variation among the populations. The genetic variation among populations was determined using the 5′-SSR primer. Populations were classified into two main groups according to the results obtained from the SSR alleles. The allele numbers ranged between 2-6 per locus, the diversity values ranged between 0.27-0.99. The morphological and molecular analyses revealed differences in terms of several quantitative characteristics among the populations examined. Similarities were also found among different E. oryzoides populations grown in different regions in terms of their morphological characteristics, the genetic diversity was found to be higher. There is a potential for the spread of resistance through gene flow owing to high genetic diversity and low differentiation among population of E. oryzoides. Under such situations to prevent further resistance spread, early watergrass management in this area should focus both on reducing seed movement among rice fields and the field management practices such as implementation of crop rotation, use of herbicides with new mode of actions or cultural methods.

An Improved Method for Assessing Simple Sequence Repeat (SSR) Variation in Echinochloa crus-galli (L.) P. Beauv (Barnyardgrass)

“…To overcome this problem, many researchers have resorted to coding each allele as a dominant marker [32][33][34][35][36][37][38], missing part of SSRs informativeness [39,40,57,58]. In fact, it would be more appropriate to treat them as codominants [39].…”

“…Since SSR alleles differ in length by many base pairs, SSR markers are well resolved on agarose gel [25,26]. SSRs are often recorded and analyzed as dominant markers [32][33][34][35][36][37][38], but this leads to loss of information about allelic variance and the presence of heterozygosity, as they are codominant [39]. However, their scoring as codominant markers in polyploid species (such as E. crus-galli) presents several challenges, as almost all population genetics software has been developed for haploid and/or diploid genotype analysis [40].…”