Abstract
Echinochloa crus-galli (L.) P. Beauv. (barnyardgrass) is one of the most noxious weeds infesting Italian rice fields. It is characterized by high genetic intraspecific variability and has developed resistance to several classes of herbicides. The aim of our study was to assess, for the first time in Italy, the genetic diversity in E. crus-galli from differently managed rice fields in the Lombardy region (Northern Italy) using eight specific SSR markers. To this purpose, an amplification protocol was optimized, testing different DNA concentrations, PCR mixtures, and temperatures. A total of 48 alleles were identified in 144 samples. SSR fingerprint analysis using R 3.6.3 software (poppr, polysat, and StAMPP) allowed us to handle SSRs as codominant and polyploid data. The results suggested that genetic richness and diversity were high. The analysis of molecular variance (AMOVA) indicated that genetic variation exists mainly between agronomic managements (47.23%) and among populations (37.01%). Hierarchical clustering and PCoA were in concordance with the identification of four distinct genetic groups. Our results confirm that SSR markers represent a valuable and affordable tool for the assessment of E. crus-galli genetic diversity and would grant useful information to plan more targeted, effective, and sustainable control strategies against barnyardgrass. The improved methodology applied here allowed us to assess the genetic variability of an allo-hexaploid species without information loss and biased results.
Highlights
Genetic variability plays a fundamental role in the adaptive response of organisms to varied environmental conditions
Chloroplast DNA intergenic spacer region nucleotide length between trnT and trnL genes differs in Echinochloa spp. (481 bp) and E. crus-galli (449 bp)
Our findings confirmed that SSR markers represent a reliable, rapid, and affordable tool to assess the genetic variability in E. crus-galli
Summary
Genetic variability plays a fundamental role in the adaptive response of organisms to varied environmental conditions. Weeds have evolved a genetic and phenetic plasticity that allows them to colonize very different ecosystems and to survive under the most adverse ecological stresses [1,2]. Weed intraspecific biodiversity assessment is fundamental for good weed control, including problematic cases of herbicide resistance [1,3]. The repeated use of herbicides that have the same mechanism of action favors the rapid evolution of herbicide resistance in weeds, aided by European regulatory constraints on the use of plant protection products (Reg. EC/1107/2009) and the practice of monoculture
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