The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice

Abstract

The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.

Figure 1.

Suspected herbicide-resistant weedy rice in a rice field previously planted with Clearfield rice along the Mississippi River Delta in Arkansas. More than 10 morphotypes of weedy rice were observed in this field, with different maturity periods. In the foreground is a typical weedy rice with pale green leaves; the rice cultivar has dark green leaves. The inset shows a weedy morphotype that matured earlier than cultivated rice.

Figure 2.

Frequency of weedy rice offspring resistant to the commercial dose of imazethapyr herbicide (two applications at 70 g ha⁻¹) from weedy plants collected in fields previously planted with Clearfield rice. Moderately resistant plants present 21% to 79% injury, and highly resistant plants present 0% to 20% injury.

Figure 3.

Frequency of imazethapyr-resistant offspring of weedy rice harvested in 2010 from commercial fields with a history of Clearfield rice classified by the hull color of the mother plant.

Figure 4.

Frequency distribution of weedy rice traits resistant to the full dose of imazethapyr (70 g ha⁻¹, two applications) at the Arkansas Rice Research and Extension Center.

Figure 5.

Principal component analysis of HR weedy rice, U.S. cultivated rice, historical SH and BHA weedy rice, and Asian aus and indica cultivars. Principal component 1 (PC1) explains 12.93% of the variance, and PC2 explains 8.61%. The inbred reference Clearfield cultivar, CL151, is labeled.

Figure 6.

Population structure of herbicide-resistant weedy rice and related groups based on GBS data. A, Population structure of HR weedy rice, weedy rice occurring prior to the widespread use of Clearfield rice (i.e. historical weedy rice), reference cultivars from Asia and the United States, and wild Oryza spp. B, Population structure of HR weedy rice, historical weedy populations, and tropical japonica cultivars.

Figure 7.

Distribution of parental population contribution to the HR weedy rice population as determined by LAMP-LD. Each horizontal bar represents a single chromosome. Colors denote possible parental populations. For all SNPs included in the analysis, the percentage of haplotypes carrying alleles from each parental population is shown.