Survey of Echinochloa weed species in rice fields using a chloroplast DNA marker and spikelet characteristics identifies accessions with possible paternal inheritance and heteroplasmy

Hexaploid Echinochloa. crus-galli var. crus-galli and tetraploid E. crus-galli var. oryzicola are major weeds in rice fields. Supplementing molecular marker data with morphological and morphometric characterization is considered a reliable method for species identification. In the present study, Echinochloa weed accessions were collected from rice fields in Tamil Nadu, India [as plants (12) or seeds (10)]. Species level identification was carried out using the distinguishing chloroplastic DNA marker, trnT-L. Eight accessions were identified as E. crus-galli consistently across T₀ and T₁ generations and twelve others over a single generation (T₀ or T₁). Spikelet length is an important feature used to distinguish E. crus-galli and E. oryzicola. Accession P1, identified as E. oryzicola, using a chloroplast DNA marker (trnT-L insertion), has a spikelet length more consistent with E. crus-galli (≤ 4 mm) than E. oryzicola. Thus, 'inconsistent' accession P1 may have inherited DNA paternally from E. oryzicola, instead of the unknown maternal donor usually reported in literature for E. crus-galli. We also report, for the first time, the occurrence of heteroplasmic variation in Echinochloa (accession D4) over two successive generations (T₀ and T₁). We also suggest a caveat in the use of morphometric spikelet characters and chloroplastic DNA marker data alone to classify Echinochloa weed species conclusively. Occurrence of paternal plastid inheritance and heteroplasmy may have implications on weed fitness, including range expansion and selective advantage(s) in a rapidly changing environment (herbicide or stress tolerance).

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-024-01525-7.