High-Throughput Phenotyping of Indirect Traits for Early-Stage Selection in Sugarcane Breeding

Abstract

One of the major limitations for sugarcane genetic improvement is the low heritability of yield in the early stages of breeding, mainly due to confounding inter-plot competition effects. In this study, we investigate an indirect selection index (Si), developed based on traits correlated to yield (indirect traits) that were measured using an unmanned aerial vehicle (UAV), to improve clonal assessment in early stages of sugarcane breeding. A single-row early-stage clonal assessment trial, involving 2134 progenies derived from 245 crosses, and a multi-row experiment representative of pure-stand conditions, with an unrelated population of 40 genotypes, were used in this study. Both experiments were screened at several stages using visual, multispectral, and thermal sensors mounted on a UAV for indirect traits, including canopy cover, canopy height, canopy temperature, and normalised difference vegetation index (NDVI). To construct the indirect selection index, phenotypic and genotypic variance-covariances were estimated in the single-row and multi-row experiment, respectively. Clonal selection from the indirect selection index was compared to single-row yield-based selection. Ground observations of stalk number and plant height at six months after planting made from a subset of 75 clones within the single-row experiment were highly correlated to canopy cover (rg = 0.72) and canopy height (rg = 0.69), respectively. The indirect traits had high heritability and strong genetic correlation with cane yield in both the single-row and multi-row experiments. Only 45% of the clones were common between the indirect selection index and single-row yield based selection, and the expected efficiency of correlated response to selection for pure-stand yield based on indirect traits (44%–73%) was higher than that based on single-row yield (45%). These results highlight the potential of high-throughput phenotyping of indirect traits combined in an indirect selection index for improving early-stage clonal selections in sugarcane breeding.

Identification of quantitative trait loci associated with canopy temperature in soybean

“…Kaler et al 14 reported a broad sense heritability (H) of 19% for CT in a diverse panel of soybean accessions evaluated in different environments using GWAS. Likewise, low to moderate broad sense heritability of CT/CTD was reported in wheat (H = 16% to 38%) 79 – 81 , in sugarcane (H = 9% to 44%) 82 , and in rice (H = 21% to 30%) 83 . The low heritability of CT/CTD in soybean and other crops indicate that this trait is highly influenced by environmental conditions 84 .…”

Genotypic variation in intrinsic transpiration efficiency correlates with sugarcane yield under rainfed and irrigated field conditions

“…Measuring gas exchange at different levels of the canopy is complicated by the decoupling effects between leaf and the atmosphere, wherein it has been shown that the leaves at the base of a canopy are potentially more decoupled from the atmosphere than top canopy leaves (Jarvis and McNaughton, 1986). The rapidly advancing aerial field phenomics technologies currently being evaluated in sugarcane breeding (Natarajan et al ., 2019) may offer solutions for the practical application of i TE for variety development.…”

“…The rapidly advancing aerial field phenomics technologies currently being evaluated in sugarcane breeding (Natarajan et al, 2019) may offer solutions for the practical application of i TE for variety development.…”

Comparison of different selection methods in the seedling stage of sugarcane breeding

“…Moreover, family selection can be improved by techniques such as high‐throughput phenotyping and genome selection. In the first situation, phenotyping is time consuming and an expensive procedure (Natarajan et al., 2019; Costa et al., 2019). The use of remote‐sensing technique based on unmanned aerial vehicle (UAV) is promising, especially, for the possibility of finding new variables to integrate in the sugarcane breeding pipeline.…”