in Feldman et al. (2017); Feldman et al. (2018) were 308 used in this study, and here the methods used are repeated. QTL mapping was 309 performed on day 27 within each treatment group using functions in the R/qtl and 310 funqtl packages (Kwak et al., 2016). The functions were called by a set of custom 311 Python and R scripts (https://github.com/maxjfeldman/foxy_qtl_pipeline). Two 312 complimentary analysis methods were utilized. First, a single QTL model genome 313 scan using Haley-Knott regression was performed to identify QTL exhibiting LOD 314 score peaks greater than a permutation-based significance threshold (α = 0.05, n = 315 1000). Second, a stepwise forward/backward selection proce
Open resource ↗maxjfeldman/foxy_qtl_pipeline · pdf-raw-page:11 lines:1-77Unverified paper record
A genetic link between leaf carbon isotope composition and whole‐plant water use efficiency in the C 4 grass Setaria
The Plant Journal · 2 Mar 2020 · 10.1111/tpj.14696
Abstract
Genetic selection for whole-plant water use efficiency (yield per transpiration; WUE plant ) in any crop-breeding programme requires high-throughput phenotyping of component traits of WUE plant such as intrinsic water use efficiency (WUE i ; CO 2 assimilation rate per stomatal conductance). Measuring WUE i by gas exchange measurements is laborious and time consuming and may not reflect an integrated WUE i over the life of the leaf. Alternatively, leaf carbon stable isotope composition (δ 13 C leaf ) has been suggested as a potential time-integrated proxy for WUE i that may provide a tool to screen for WUE plant . However, a genetic link between δ 13 C leaf and WUE plant in a C 4 species has not been well established. Therefore, to determine if there is a genetic relationship in a C 4 plant between δ 13 C leaf and WUE plant under well watered and water-limited growth conditions, a high-throughput phenotyping facility was used to measure WUE plant in a recombinant inbred line (RIL) population created between the C 4 grasses Setaria viridis and S. italica. Three quantitative trait loci (QTL) for δ 13 C leaf were found and co-localized with transpiration, biomass accumulation, and WUE plant . Additionally, WUE plant for each of the δ 13 C leaf QTL allele classes was negatively correlated with δ 13 C leaf , as would be predicted when WUE i influences WUE plant . These results demonstrate that δ 13 C leaf is genetically linked to WUE plant , likely to be through their relationship with WUE i , and can be used as a high-throughput proxy to screen for WUE plant in these C 4 species.
Plant phenotyping relevance
葉の炭素安定同位体比を全植物体の水利用効率の高スループット代理指標として検証し、WUEとの遺伝的関連を評価しており、表現型取得・スクリーニング法が中心的です。
abstractleaf carbon stable isotope composition (δ 13 C leaf ) has been suggested as a potential time-integrated proxy for WUE i that may provide a tool to screen for WUE plant
Code and data availability
The paper's QTL analysis was performed with the authors' custom Python and R scripts, publicly deposited on GitHub (foxy_qtl_pipeline). No public phenotype dataset URL is stated in the supplied blocks.
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