Remote-Sensing-Combined Haplotype Analysis Using Multi-Parental Advanced Generation Inter-Cross Lines Reveals Phenology QTLs for Canopy Height in Rice.

Abstract

High-throughput phenotyping systems with unmanned aerial vehicles (UAVs) enable observation of crop lines in the field. In this study, we show the ability of time-course monitoring of canopy height (CH) to identify quantitative trait loci (QTLs) and to characterise their pleiotropic effect on various traits. We generated a digital surface model from low-altitude UAV-captured colour digital images and investigated CH data of rice multi-parental advanced generation inter-cross (MAGIC) lines from tillering and heading to maturation. Genome-wide association studies (GWASs) using the CH data and haplotype information of the MAGIC lines revealed 11 QTLs for CH. Each QTL showed haplotype effects on different features of CH such as stage-specificity and constancy. Haplotype analysis revealed relationships at the QTL level between CH and, vegetation fraction and leaf colour [derived from UAV red–green–blue (RGB) data], and CH and yield-related traits. Noticeably, haplotypes with canopy lowering effects at qCH1-4, qCH2, and qCH10-2 increased the ratio of panicle weight to leaf and stem weight, suggesting biomass allocation to grain yield or others through growth regulation of CH. Allele mining using gene information with eight founders of the MAGIC lines revealed the possibility that qCH1-4 contains multiple alleles of semi-dwarf 1 (sd1), the IR-8 allele of which significantly contributed to the “green revolution” in rice. This use of remote-sensing-derived phenotyping data into genetics using the MAGIC lines gives insight into how rice plants grow, develop, and produce grains in phenology and provides information on effective haplotypes for breeding with ideal plant architecture and grain yield.

Plant phenotyping relevance

UAV画像からデジタル表面モデルと時系列のイネ群落高を抽出し、遺伝解析に利用する高スループット表現型計測が研究の中心であるため。

Code and data availability

The paper's supplementary material explicitly contains the paper-specific phenotyping datasets (Supplementary Data 1: canopy height data; Supplementary Data 2: haplotype data; Supplementary Data 3-4: haplotype counts and time-course effects) used for the haplotype-based GWAS, and is publicly available at the Frontiers'