Statistical Methods for Plant Variety Evaluation

Transcription

1 Statistical Methods for Plant Variety Evaluation JOIN US ON THE INTERNET VIA WWW, GOPHER, FTP OR WWW: GOPHER: FTP: gopher.thomson.com ftp.thomson.com A service of loop

2 PLANT BREEDING SERIES 3 STATISTICAL METHODS FOR PLANT VARIETY EVALUATION Edited by RA. Kempton and P.N. Fox The present book is the third in the Plant Breeding Series published by Chapman & Hall and follows the very favourable reception that the two earlier volumes have already received. The first book, Plant Breeding: Principles and prospects, edited by Hayward, Bosemark and Romagosa, set a wide ranging and authoritative broad view of techniques and approaches being adopted in modern plant breeding. The second, Selection Methods in Plant Breeding, by Bos and Caligari, was written to help further secure the scientific basis underlying selection methods as applied in practical plant breeding. This third book tackles the vitally important area of statistical techniques for data handling and analyses along with, of course, the trial designs needed specifically by the modern plant breeder. The efficiency and effectiveness of plant breeding and selection programmes have often been left unexamined. As a consequence many breeding programmes have made much less impact than they otherwise might have done. Thus, for example, imagined differences form the basis for selection; systematic biases are unwittingly included in the trial designs because the necessary application of statistics has been ignored. Often, because plant breeders in the past have been unwilling to make themselves sufficiently acquainted with the underlying features and philosophy of statistical application (as opposed to theory), they have been unable to at least adopt rudimentary designs for their trials which would allow meaningful analyses. This philosophy has changed greatly over recent times but now, with the widespread availability of computers, thoughts and possibilities are moving very quickly. This book thus aims to provide a timely and well balanced account of statistical methods, data management and handling allied to the potential for effective experimental designs specifically with plant breeding in mind. As noted in the earlier books the need for plant breeders to be successful has never been greater. The potential future population growth must fill all of us with concern and with a clear indication for the absolute need for plant breeders to succeed. The adoption of new and potentially powerful techniques, such as those provided by biotechnology, plant transformation and molecular biology, are well perceived. But these will only make any real and practical input when applied within the context of more complete approaches to plant breeding. Foremost among the integrated requirements for success is the ability to evaluate any material produced in trials which give clear, informative and applicable results - the need for Statistical Methods in Plant Variety Evaluation is obvious. The present book is aimed, as the first two were, not only at the student who is learning the subject of plant breeding but also the breeder who is trying to actually improve our crop species. It has been written to make clear the exciting possibilities for exploiting modern statistical methods to further the aims central to plant breeding worldwide. Peter DS. Caligari Plant Breeding Series Editor

3 Statistical Methods for Plant Variety Evaluation Edited by R.A. Kempton Biomathematics and Statistics Scotland P.N. Fox CIMMYT Mexico Coordinating editor M. Cerezo, CIHEAM, Zaragoza, Spain CIHEAM CHAPMAN &. HALL London Weinheim. New York. Tokyo. Melbourne. Madras

4 Published by Chapman & Hall, 2-6 Boundary Row, London SEI 8HN, UK Chapman & Hall, 2-6 Boundary Row, London SE1 8HN, UK Chapman & Hall GmbH, Pappelallee 3, Weinheim, Germany Chapman & Hall USA, 115 Fifth Avenue, New York, NY 10003, USA Chapman & Hall Japan, ITO-Japan, Kyowa Building, 3F, Hirakawacho, Chiyoda-ku, Tokyo 102, Japan Chapman & Hall Australia, 102 Dodds Street, South Melbourne, Victoria 3205, Australia Chapman & Hall India, R. Seshadri, 32 Second Main Road, CIT East, Madras , India First edition Chapman & Hall Softcover reprint of the hardcover 1 st edition 1997 Typeset in 9.5/11.5pt Palatino by Columns Design Ltd, Reading ISBN-13: DOl: / e-isbn-13: Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the UK Copyright Designs and Patents Act, 1988, this publication may not be reproduced, stored, or transmitted, in any form or by any means, without the prior permission in writing of the publishers, or in the case of reprographic reproduction only in accordance with the terms of the licenc;es issued by the Copyright Licensing Agency in the UK, or in accordance with the terms of licences issued by the appropriate Reproduction Rights Organization outside the UK. Enquiries concerning reproduction outside the terms stated here should be sent to the publishers at the London address printed on this page. The publisher makes no representation, express or implied, with regard to the accuracy of the information contained in this book and cannot accept any legal responsibility or liability for any errors or omissions that may be made. A Catalogue record for this book is available from the British Library Library of Congress Catalog Card Number: SPrinted on permanent acid-free text paper, manufactured in accordance with ANSI/NISO Z and ANSI/NISO Z (Permanence of Paper)

5 Contents Contributors Foreword Preface viii IX xi 1 Introduction 1 R.A. Kempton and P.N. Fox 1.1 Change and challenges Managing the information Statistical design of the selection programme Statistical models and prediction Impact of genotype by environment interaction Summary Nomenclature 8 2 Field plot technique 9 P. Portmann and H. Ketata 2.1 Introduction Terminology Within-location variation Inter-plot interference The plot Replication Trial management Trial layout Data Data collection Data analysis 17 3 Data management and validation 19 PN. Fox, R. Mead, M. Talbot and J.D. Corbett 3.1 Introduction Data management Validation of trial data 25 4 Design of plant breeding trials 40 R. Mead 4.1 Introduction Experimental design concepts and model assumptions Plots, replication, randomization, covariance Blocking - control and adjustment The construction of incomplete block designs Precision Multiple levels of information 58

6 vi Contents 4.8 Rowand column designs Trial designs for spatial analysis Multilocation experiments Additional factors 67 5 Spatial analysis 68 AC. Gleeson 5.1 Why spatial analysis? Spatial autocorrelation Sample spatial correlations for uniformity trials Models for the analysis of field trial data Stationarity One-dimensional spatial analysis Estimation Assessing model adequacy Extension to two-dimensional spatial analysis Example Conclusion 83 6 Unreplicated trials 86 R.A Kempton and AC. Gleeson 6.1 Introduction Local control using check plots Local control from blocking test plots Local control by spatial analysis Conclusions Interference between plots 101 R.A Kempton 7.1 Introduction Reducing interference through design Modelling interference Adjusting for interference Summary Multi-environment testing and genotype x environment interaction 117 P.N. Fox, J. Crossa and I. Romagosa 8.1 What is genotype x environment interaction? Implications for breeding programmes Univariate data analysis and exploration of genotype performance Multivariate exploration of relationships among environments and among genotypes Information extraction versus computational complexity Analysis of series of variety trials 139 HD. Patterson 9.1 Introduction Notation and terminology 140

7 Contents vii 9.3 FITCON and REML Analysis of Immer's balanced series Method of direct differences Incomplete tables and the adjustment of variety means An incomplete three-way table Other models Resource allocation for selection systems 162 M. Talbot 10.1 Introduction Variation in trials system Precision of genotype means Criteria for assessing the efficiency of the programme Other issues in resource allocation Conclusions 174 References 175

8 Contributors J.D. Corbett Integrated Information Management Laboratory Blackland Research Center Texas A & M University System 808 E. Blackland Road Temple Texas USA J. Crossa International Maize and Wheat Improvement Center (ClMMYT) Lisboa 27, Colonia Juarez Apartado Postal Mexico, DF Mexico PN. Fox International Maize and Wheat Improvement Center (ClMMYT) Lisboa 27, Colonia Juarez Apartado Postal Mexico, DF Mexico A.c. Gleeson NSW Agriculture Division of Corporate Services 161 Kite Street Locked Bag 21 Orange NSW 2800 Australia RA. Kempton Biomathematics & Statistics Scotland James Clerk Maxwell Building The King's Buildings University of Edinburgh Edinburgh EH9 3JZ UK H. Ketata International Center for Agricultural Research in the Dry Areas (ICARDA) Germplasm Program PO Box 5466 Aleppo Syria R Mead The University of Reading Department of Applied Statistics PO Box 240 Earley Gate Reading RG6 6FN UK H.D. Patterson 15 Kings Grove Longniddry East Lothian EH32 OQW UK P. Portmann Agriculture Western Australia Crop Breeding 3 Baron-Hay Court South Perth Western Australia 6151 Australia 1. Romagosa Centre UdL - IRTA Departamento de Producci6n Vegetal Avenida Rovira Roure Lleida Spain M. Talbot Biomathematics & Statistics Scotland James Clerk Maxwell Building The King's Buildings University of Edinburgh Edinburgh EH9 3JZ UK

9 Foreword The International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM), established in 1962, is an intergovernmental organization of fourteen countries: Albania, Algeria, Egypt, France, Greece, Italy, Lebanon, Malta, Morocco, Portugal, Spain, Tunisia, Turkey and Yugoslavia. Four institutes (Bari, Italy; Chania, Greece; Montpellier, France and Zaragoza, Spain) provide post-graduate education at the Master of Science level. CIHEAM promotes research networks on Mediterranean agricultural priorities, supports the organization of specialized education in member countries, holds seminars and workshops bringing together technologists and scientists involved in Mediterranean agriculture and regularly produces diverse publications including the series 'Options Mediterraneennes'. Through these activities, CIHEAM promotes North/South dialogue and international co-operation for agricultural development in the Mediterranean region. Plant breeding is, since 1982, one of the fields in which CIHEAM is conducting a programme of training and promotion of research, through its Mediterranean Agronomic Institute of Zaragoza. The programme includes a one-year advanced specialization course, a series of two-week courses for professionals, and support for collaborative research activities in Mediterranean-relevant species. Many of these activities are organized in collaboration with national and international institutions. The publication in 1993 of Plant Breeding. Principles and Prospects, which initiated the Chapman & Hall's Plant Breeding Series, has become an important feature of CIHEAM's plant breeding programme. We are now pleased to add a further volume to that series: the present book, Statistical Methods for Plant Variety Evaluation. As was the case for the first publication, Statistical Methods for Plant Variety Evaluation originates from one of CIHEAM's courses. The course was organized in collaboration with the International Center for Agricultural Research in the Dry Areas (ICARDA) and the International Maize and Wheat Improvement Center (CIMMYT) to deal with the important issue of the improvement of the economic efficiency of plant evaluation trials. The good interaction between a group of lecturers, internationally known for their expertise in this field, and an international group of professionals participating in two editions of the course, has produced excellent results and, as the editors have underlined, has helped to motivate the authors to produce this book. In their preface, the editors present the objectives and the contents of the book, and describe the essential elements in its creation. This description shows clearly that the book is the result of a combination of contributions and of efforts from individuals and institutions. We would therefore like to thank all those who have directly or indirectly participated in this project. Our special thanks go to all the authors of the chapters for their valuable con-

10 x Foreword tributions and for the interest they have shown in this endeavour, and very specially to RA. Kempton and PN. Fox, the editors who, with their enthusiasm, dedication and skill, have made this publication possible. We acknowledge, on this occasion too, the collaboration and interest of Chapman & Hall as well as the Series Editor, Professor Caligari, The University of Reading. We would like to express our wish that this book will help all those who read it, and especially plant breeders, to plan more efficient experiments and open new opportunities for collaboration. Miguel Valls Director Mediterranean Agronomic Institute of Zaragoza, Spain

11 Preface Plant breeding is experiencing major changes in technology and relative economics, the full strategic implications of which are not yet appreciated. But one point is clear: as the costs of generating field, glasshouse and laboratory information continue to rise, the costs of managing that information are falling. Plant breeders must respond by ensuring that the data are collected efficiently using the best experimental practice and trial designs, and are fully utilized using modern methods for their management, exchange and analysis. The genesis of the book was a course presented in 1991 at the International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM), Zaragoza, Spain, in collaboration with two international agricultural research institutes, the International Maize and Wheat Improvement Center (CIM MYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA). Lecturers came from these institutes, from the Scottish Agricultural Statistics Service (now Biomathematics and Statistics Scotland), the New South Wales Department of Agriculture, Australia, and the Universities of Lleida, Spain, and Reading, UK. The strength of the course lay in the mixing of statisticians, computer specialists and plant breeders - 'tool makers' with 'tool users'. The high level of interest in the course, which was three times over-subscribed, and the geographical diversity of the 30 participants, who came from 19 countries, demonstrated a widespread awareness of the importance of modern statistical and data management techniques. During the computer practical sessions many participants arrived at new biological understanding of their own data. This demonstrated a lasting impact and the course was repeated in We thank participants in both courses for their stimulating questions and suggestions. Their interest and enthusiasm helped motivate the lecturers to produce this book. The Director and staff at the CIHEAM training centre, particularly Manuela Cerezo and Maria Navarro, assisted the participants and lecturers with efficiency, tact and humour. This book describes modern statistical and trial management techniques for field evaluation of genotypic performance. It focuses on the distinctive goals of plant breeders and the technical problems that they face at each stage of selection. It includes detailed description of field plot techniques and designs for plant breeding trials; of statistical methods for spatial analysis and controlling inter-plot competition; of methods for multi-environment testing and analysis of genotype by environment interaction; and of efficient partitioning of resources among the different stages of selection. Individual chapters have been edited to provide cross-referencing and eliminate inconsistencies, though the careful reader will notice differences in approach and emphasis which reflect the working backgrounds and concerns of particular authors. Inevitably, a single volume cannot deal with all aspects

12 xii Preface of plant breeding. In particular, we say nothing about the selection of parents for a crossing programme or the statistical techniques in biometrical genetics, linkage analysis and molecular sequencing which can assist with this choice. Emphasis, moreover, is on selection for yield in annual crops, where the authors' experiences mainly lie, and we do not consider selection for multiple characters in depth or for a single character over several harvests. With these exceptions, however, the book provides a comprehensive treatment of statistical issues which are increasingly important to a successful breeding programme. R.A. Kempton and P.N. Fox Zaragoza, Spain