Comparing simple root phenotyping methods on a core set of rice genotypes

Abstract

Interest in belowground plant growth is increasing, especially in relation to arguments that shallow-rooted cultivars are efficient at exploiting soil phosphorus while deep-rooted ones will access water at depth. However, methods for assessing roots in large numbers of plants are diverse and direct comparisons of methods are rare. Three methods for measuring root growth traits were evaluated for utility in discriminating rice cultivars: soil-filled rhizotrons, hydroponics and soil-filled pots whose bottom was sealed with a non-woven fabric (a potential method for assessing root penetration ability). A set of 38 rice genotypes including the OryzaSNP set of 20 cultivars, additional parents of mapping populations and products of marker-assisted selection for root QTLs were assessed. A novel method of image analysis for assessing rooting angles from rhizotron photographs was employed. The non-woven fabric was the easiest yet least discriminatory method, while the rhizotron was highly discriminatory and allowed the most traits to be measured but required more than three times the labour of the other methods. The hydroponics was both easy and discriminatory, allowed temporal measurements, but is most likely to suffer from artefacts. Image analysis of rhizotrons compared favourably to manual methods for discriminating between cultivars. Previous observations that cultivars from the indica subpopulation have shallower rooting angles than aus or japonica cultivars were confirmed in the rhizotrons, and indica and temperate japonicas had lower maximum root lengths in rhizotrons and hydroponics. It is concluded that rhizotrons are the preferred method for root screening, particularly since root angles can be assessed.

Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance

“…In general it is reported that rooting depth of rice accessions differs between subpopulations. For example Shrestha et al (2014) report that rhizotron screens rank subgroups in the order aus  >  tropical japonica  >  indica  ≈  temperate japonica for maximum root length which was in agreement with an earlier report of Lafitte et al (2001). This order has been confirmed testing the RDP1 with the herbicide screen (unpublished results) where aus has the highest average scores, followed by tropical japonica with indica and temperate japonica both similarly low.…”

“…6) whereas the strongest correlation for shoot traits was with shoot length at day 35 ( r  = 0.586). Figure 6 shows that check varieties behaved as expected (as shown in Shrestha et al 2014), with Black Gora very long rooted, Azucena reasonably long rooted, IR 64 reasonable short rooted and Bala very short rooted. There were Sri Lankan landraces across the spectrum of these check varieties including some very long and very short rooted.

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“…A total of 32 Sri Lankan landraces plus check cultivars Azucena, Bala, Black Gora and IR 64 were assessed in a hydroponic system previously described (Price et al 1997, Shrestha et al 2014). The Sri Lanka landraces were chosen to represent 11 with the highest herbicide scores, 11 with lowest scores and 10 with near average scores.…”

“…A total of 12 genotypes were assessed for root traits using the rhizotron system that is described in detail in Price et al (2012) which has been widely used to assess rice (Price et al 2002; Shrestha et al 2014). Four replicates were arranged in completely randomised blocks.…”

Phenotyping roots in darkness: disturbance-free root imaging with near infrared illumination

“…As an alternative, two dimensional (2D) root imaging in rhizotrons enables the quantification of root growth along the interface between soil and a transparent cover. This method is amenable to high throughput and provides very comprehensive information on root system architecture with limitations on tall plants or late developmental stages (Nagel et al 2012;Shrestha et al 2014).…”