SmartGrain: High-Throughput Phenotyping Software for Measuring Seed Shape through Image Analysis
SmartGrain: High-Throughput Phenotyping Software for Measuring Seed Shape through Image Analysis
复制标题
DOI：
10.1104/pp.112.205120
复制
发表时间：
2012-12-01
期刊：
影响因子：
7.4
通讯作者：
Yano, Masahiro
中科院分区：
文献类型：
--
作者：
Tanabata, Takanari;Shibaya, Taeko;Yano, Masahiro
种子的形状和大小是最重要的农艺性状之一，因为它们影响产量和市场价格。为了获得准确的种子大小数据，需要进行大量的测量，因为同一种植物的种子大小差异不大。为了促进植物育种中种子形态的遗传分析和选择，需要高效、可靠、高通量的种子表型分析方法。我们开发了SmartGrain软件，用于高通量测量种子形状。该软件采用了一种新的图像分析方法，减少了种子制备和图像捕获所需的时间。从数字图像中自动识别种子轮廓，并计算种子的长度、宽度、面积、周长等形状参数。为了验证该软件的有效性，我们利用粳稻品种“光”（Koshihikari）和“日本裸”（Nipponbare）的回交自交系对水稻（Oryza sativa）的种子形状进行了数量性状位点（QTL）分析，结果显示种子形状差异不大。SmartGrain自动去除草坪和花梗区域，并检测到6个形状参数的多个qtl。在11号染色体上检测到的与种子长度有关的QTL在回交后代中证实了等位基因效应；cv Nipponbare等位基因增加了种子长度，从而增加了种子重量。SmartGrain的高通量测量减少了采样误差，并使区分种子形状差异很小的品系成为可能。SmartGrain不仅能准确识别水稻的种子，还能识别包括拟南芥（Arabidopsis thaliana）在内的其他几种种子。该软件对研究人员是免费的。
Seed shape and size are among the most important agronomic traits because they affect yield and market price. To obtain accurate seed size data, a large number of measurements are needed because there is little difference in size among seeds from one plant. To promote genetic analysis and selection for seed shape in plant breeding, efficient, reliable, high-throughput seed phenotyping methods are required. We developed SmartGrain software for high-throughput measurement of seed shape. This software uses a new image analysis method to reduce the time taken in the preparation of seeds and in image capture. Outlines of seeds are automatically recognized from digital images, and several shape parameters, such as seed length, width, area, and perimeter length, are calculated. To validate the software, we performed a quantitative trait locus (QTL) analysis for rice (Oryza sativa) seed shape using backcrossed inbred lines derived from a cross between japonica cultivars Koshihikari and Nipponbare, which showed small differences in seed shape. SmartGrain removed areas of awns and pedicels automatically, and several QTLs were detected for six shape parameters. The allelic effect of a QTL for seed length detected on chromosome 11 was confirmed in advanced backcross progeny; the cv Nipponbare allele increased seed length and, thus, seed weight. High-throughput measurement with SmartGrain reduced sampling error and made it possible to distinguish between lines with small differences in seed shape. SmartGrain could accurately recognize seed not only of rice but also of several other species, including Arabidopsis (Arabidopsis thaliana). The software is free to researchers.