Just as standardized Latin names are used in biological nomenclature, it is equally important that standardization be used in assigning names to measured traits in plant breeding to ensure proper communication between researchers of the same field. Ontology is therefore important in marker assisted breeding (MAB). Also important in MAB is measuring phenotype traits with the appropriate methods to ensure a correct interpretation of the results. Like in other biology experiments statistics is involved in the experimental design and in the analysis of the collected data. However for statistics to be applied meaningfully a working knowledge of its application and the most appropriate statistics tool to use for a specific analysis is required.

This lesson is written for plant breeders and professionals working with plant breeders. It is not intended to be a comprehensive guide to phenotyping, simply special notes on phenotyping specifically in the context of molecular breeding. It assumes basic knowledge of plant breeding and phenotyping, and the kinds of traits that plant breeders’ phenotype. This elesson module is organized into three parts:

Part 1: Phenotype Vocabulary in MAB

  • Naming your traits
  • Ontology
  • Available ontologies

Part 2: Phenotyping Assays

  • Marker-trait Correlations and Phenotyping assays

Part 3: Data Analysis in Phenotyping for MAB

  • Kinds of data and statistic test applicable
  • Checklist before a Statistical Analysis

This module ends with a summary of the eLesson and a quiz which randomly pulls questions from a quiz bank. The lesson also ends with an introduction to the next sequential module.  If you correctly answer 80% of the quiz questions correctly, you will earn an electronic badge of completion which will be emailed to you directly.  You may retake the quiz, as you wish.  On average, it will take participants approximately 20-45 mins to complete this eLesson, including the quiz.

Goals and Objectives

The overall goals of this lesson/module are that you will have an increased understanding of the following:

  • Ontology in MAB
  • Phenotyping Assays
  • Ways of scoring data when phenotyping for MAB

After completing this lesson/module, you will be able to explain, describe, discuss, recognize, and/or apply knowledge understanding of the following:

1. Proper usage of Phenotype vocabulary for effective communication

2. Marker-traits correlations and phenotyping assays

3. Understand the choices in types of data in phenotyping for MAB.

Copyright 2014

This eLesson was supported in part by the National Research Initiative Competitive Grants CAP project 2011-68002-30029 from the USDA National Institute of Food and Agriculture, administered by the University of California-Davis. Any opinions, findings, conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the USDA -NIFA.