Indirect selection using reference and probe genotype performance in multi-environment trials
Ky L. Mathews A B C , Richard Trethowan C D , Andrew W. Milgate E F , Thomas Payne C , Maarten van Ginkel C G , Jose Crossa C , Ian DeLacy B , Mark Cooper B H and Scott C. Chapman A I
+ Author Affiliations
- Author Affiliations
A CSIRO Plant Industry, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, Qld 4067, Australia.
B School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, St. Lucia, Qld 4072, Australia.
C International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 México, D.F., México.
D Present address: Plant Breeding Institute, The University of Sydney, PMB 11 Camden, NSW 2570, Australia.
E EH Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University).
F Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Private Mail Bag, Pine Gully Road, Wagga Wagga, NSW 2650, Australia.
G Present address: International Centre for Agricultural Research in the Dryland Areas, PO Box 5466, Aleppo, Syria.
H Present address: Pioneer Hi-Bred International Inc., PO Box 552, Johnston, IA 50131, USA.
I Corresponding author. Email: Scott.Chapman@csiro.au
Crop and Pasture Science 62(4) 313-327 https://doi.org/10.1071/CP10318
Submitted: 28 September 2010 Accepted: 15 March 2011 Published: 19 April 2011
Abstract
There is a substantial challenge in identifying appropriate cultivars from databases for introduction into a breeding program. We propose an indirect selection procedure that illustrates how strategically designed multi-environment trials, linked to historical performance databases, can identify germplasm to meet objectives of plant breeding programs.
Two strategies for indirect selection of germplasm from the International Wheat and Maize Improvement Center’s (CIMMYT) trial database were developed based on reference and probe genotype sets included in the International Adaptation Trial (IAT). The IAT was designed to improve the understanding of relationships among global spring wheat (Triticum spp.) locations. Grain yield (t/ha) data were collated from 183 IAT trials grown in 40 countries (including Australia) between 2001 and 2004.
The reference genotype set strategy used the genetic correlations among locations in the IAT to identify locations similar to a target environment. For a key southern Australian breeding location, Roseworthy, the number of cultivars targeted for selection was reduced to 35% of the original 1252. The Irrigated Winter Cereals Trials (2008–09) aimed to identify high yield potential lines in south-eastern Australian irrigated environments. Thirty-five CIMMYT cultivars identified using the reference genotype selection strategy were grown in this trial series. In all trials, the proportion of CIMMYT cultivars in the top 20% yielding lines exceeded the expected proportion, 0.20.
The probe genotype strategy utilised contrasting line yield responses to assess the occurrence of soil-borne stresses such as root lesion nematode (Pratylenchus thorneii) and boron toxicity. For these stresses, the number of targeted cultivars was reduced to 25% and 83% of the original 1252, respectively.
Additional keywords: environment characterisation, genotype-by-environment interaction, response to selection.
References
Brancourt-Hulmel M, Lecomte C, Meynard JM (1999) A diagnosis of yield-limiting factors on probe genotypes for characterizing environments in winter wheat trials. Crop Science 39, 1798–1808.| A diagnosis of yield-limiting factors on probe genotypes for characterizing environments in winter wheat trials.Crossref | GoogleScholarGoogle Scholar |
Brennan JP, Fox PN (1998) Impact of CIMMYT varieties on the genetic diversity of wheat in Australia, 1973–1993. Australian Journal of Agricultural Research 49, 175–178.
| Impact of CIMMYT varieties on the genetic diversity of wheat in Australia, 1973–1993.Crossref | GoogleScholarGoogle Scholar |
Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2009) ‘ASReml-R reference manual: mixed models for S language environments.’ 3rd edn (The State of Queensland, Department of Primary Industries and Fisheries: Brisbane, Qld)
Cartwright B, Zarcinas BA, Spouncer LR (1986) Boron toxicity in South Australian barley crops. Australian Journal of Agricultural Research 37, 351–359.
| Boron toxicity in South Australian barley crops.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaL28Xltlartr0%3D&md5=136b60e4691ff54dec76ed18c1e839a2CAS |
Cooper M, Delacy IH, Byth DE, Woodruff DR (1993) Predicting grain-yield in Australian environments using data from CIMMYT international wheat performance trials. 2. The application of classification to identify environmental relationships which exploit correlated response to selection. Field Crops Research 32, 323–342.
| Predicting grain-yield in Australian environments using data from CIMMYT international wheat performance trials. 2. The application of classification to identify environmental relationships which exploit correlated response to selection.Crossref | GoogleScholarGoogle Scholar |
Cooper M, Fox PN (1996) Environmental characterization based on probe and reference genotypes. In ‘Plant adaptation and crop improvement’. (Eds M Cooper, GL Hammer) pp. 529–547. (CAB International: Wallingford, UK)
Cooper M, Woodruff DR (1993) Predicting grain-yield in Australian environments using data from CIMMYT international wheat performance trials. 3. Testing predicted correlated response to selection. Field Crops Research 35, 191–204.
| Predicting grain-yield in Australian environments using data from CIMMYT international wheat performance trials. 3. Testing predicted correlated response to selection.Crossref | GoogleScholarGoogle Scholar |
Fox PN, Rosielle AA (1982) Reference sets of genotypes and selection for yield in unpredictable environments. Crop Science 22, 1171–1175.
| Reference sets of genotypes and selection for yield in unpredictable environments.Crossref | GoogleScholarGoogle Scholar |
Gilmour AR, Cullis BR, Verbyla AP (1997) Accounting for natural and extraneous variation in the analysis of field experiments. Journal of Agricultural, Biological & Environmental Statistics 2, 269–293.
| Accounting for natural and extraneous variation in the analysis of field experiments.Crossref | GoogleScholarGoogle Scholar |
Jefferies SP, Pallotta MA, Paull JG, Karakousis A, Kretschmer JM, Manning S, Islam AKMR, Langridge P, Chalmers KJ (2000) Mapping and validation of chromosome regions conferring boron toxicity tolerance in wheat (Triticum aestivum). Theoretical and Applied Genetics 101, 767–777.
| Mapping and validation of chromosome regions conferring boron toxicity tolerance in wheat (Triticum aestivum).Crossref | Triticum aestivum).&journal=Theoretical and Applied Genetics&volume=101&pages=767-777&publication_year=2000&author=SP%20Jefferies&hl=en&doi=10.1007/s001220051542" target="_blank" rel="nofollow noopener noreferrer" class="reftools">GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3cXosFyhurg%3D&md5=912311a42449bfd0b77f933705ad90afCAS |
Kalayci M, Alkan A, Cakmak I, Bayramoglu O, Yilmaz A, Aydin M, Ozbek V, Ekiz H, Ozberisoy F (1998) Studies on differential response of wheat cultivars to boron toxicity (Reprinted from Wheat: Prospects for global improvement, 1998). Euphytica 100, 123–129.
| Studies on differential response of wheat cultivars to boron toxicity (Reprinted from Wheat: Prospects for global improvement, 1998).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1cXivFWqsrY%3D&md5=6beba7ac69ca4042437a3fe623178a79CAS |
Mathews KL, Chapman SC, Trethowan R, Pfeiffer W, van Ginkel M, Crossa J, Payne T, DeLacy I, Fox PN, Cooper M (2007) Global adaptation patterns of Australian and CIMMYT spring bread wheat. Theoretical and Applied Genetics 115, 819–835.
| Global adaptation patterns of Australian and CIMMYT spring bread wheat.Crossref | GoogleScholarGoogle Scholar | 17768603PubMed |
Mathews KL, Chapman SC, Trethowan R, Singh RP, Crossa J, Pfeiffer W, van Ginkel M, DeLacy I (2006) Global adaptation of spring bread and durum wheat lines near-isogenic for major reduced height genes. Crop Science 46, 603–613.
| Global adaptation of spring bread and durum wheat lines near-isogenic for major reduced height genes.Crossref | GoogleScholarGoogle Scholar |
McCouch S (2004) Diversifying selection in plant breeding. PLoS Biology 2, e347
| Diversifying selection in plant breeding.Crossref | GoogleScholarGoogle Scholar | 15486582PubMed |
Moody DB, Rathjen AJ, Cartwright B (1993) Yield evaluation of a gene for boron tolerance. In ‘Genetic aspects of plant mineral nutrition’. (Eds P Randall, E Delhaize, RA Richards, R Munns) pp. 363–366. (Kluwer Academic Publishers: Dordrecht, The Netherlands)
Nicol JM (2002) Important nematode pests of cereals. In ‘Wheat production and improvement’. FAO Plant Production and Protection Series. (Ed. BC Curtis) pp. 345–366. (FAO: Rome)
Nicol JM, Ortiz-Monasterio I (2004) Effects of the root-lesion nematode, Pratylenchus thornei, on wheat yields in Mexico. Nematology 6, 485–493.
| Effects of the root-lesion nematode, Pratylenchus thornei, on wheat yields in Mexico.Crossref | Pratylenchus thornei, on wheat yields in Mexico.&journal=Nematology&volume=6&pages=485-493&publication_year=2004&author=JM%20Nicol&hl=en&doi=10.1163/1568541042665223" target="_blank" rel="nofollow noopener noreferrer" class="reftools">GoogleScholarGoogle Scholar |
O’Brien L, Morrell M, Wrigley C, Appels R (2001) Genetic pool of Australian wheats. In ‘The world wheat book: a history of wheat breeding’. Ch. 23. (Eds AP Bonjean, JA William) pp. 611–648. (Intercept Ltd: London)
Parker GD, Fox PN, Langridge P, Chalmers K, Whan B, Ganter PF (2002) Genetic diversity within Australian wheat breeding programs based on molecular and pedigree data. Euphytica 124, 293–306.
| Genetic diversity within Australian wheat breeding programs based on molecular and pedigree data.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38XksFeitLY%3D&md5=838cd32e4635a629c536f247465e642aCAS |
Payne TS, Skovmand B, Lopez CG, Brandon E, McNab A (2002) ‘The International Wheat Information System (IWIS™), Version 4, 2001.’ (CD-ROM) (CIMMYT: Mexico, D.F.)
Petersen RG (1977) Use and misuse of multiple comparison procedures. Agronomy Journal 69, 205–208.
| Use and misuse of multiple comparison procedures.Crossref | GoogleScholarGoogle Scholar |
Punchana S, Jamjod S, Rerkasem B (2004) Response to boron toxicity in boron efficient and inefficient wheat genotypes. In ‘New directions for a diverse planet: 4th International Crop Science Congress’. Brisbane, Qld. (Eds A Fischer, N Turner, J Angus, CL McIntyre, M Robertson, A Borrell, D Lloyd) (CD-ROM) (The Regional Institute Ltd: Gosford, NSW)
R Development Core Team (2009) ‘R: A language and environment for statistical computing.’ (R Foundation for Statistical Computing: Vienna) URL: www.R-project.org
Rajaram SM, van Ginkel M, Fischer RA (1994) CIMMYT’s wheat breeding mega-environments (ME). In ‘Proceedings of the 8th International Wheat Genetics Symposium’. 1994, Beijing, China, pp. 1101–1106. (Publishing Press: Beijing)
Reynolds MP, Borlaug NE (2006) Impacts of breeding on international collaborative wheat improvement. The Journal of Agricultural Science 144, 3–17.
| Impacts of breeding on international collaborative wheat improvement.Crossref | GoogleScholarGoogle Scholar |
Sivapalan S, O’Brien L, Ortiz-Ferrara G, Hollamby GJ, Barclay I, Martin PJ (2003) A comparative study for yield performance and adaptation of some Australian and CIMMYT/ICARDA wheat genotypes grown at selected locations in Australia and the WANA region. Australian Journal of Agricultural Research 54, 91–100.
| A comparative study for yield performance and adaptation of some Australian and CIMMYT/ICARDA wheat genotypes grown at selected locations in Australia and the WANA region.Crossref | GoogleScholarGoogle Scholar |
Smith A, Cullis B, Thompson R (2001) Analyzing variety by environment data using multiplicative mixed models and adjustments for spatial field trend. Biometrics 57, 1138–1147.
| Analyzing variety by environment data using multiplicative mixed models and adjustments for spatial field trend.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD38%2Fjs12jsw%3D%3D&md5=c109edcee21f0f7a886e80dd492d8c5eCAS | 11764254PubMed |
Taylor SP, Vanstone VA, Ware AH, McKay AC, Szot D, Russ MH (1999) Measuring yield loss in cereals caused by root lesion nematodes (Pratylenchus neglectus and P. thornei) with and without nematicide. Australian Journal of Agricultural Research 50, 617–622.
| Measuring yield loss in cereals caused by root lesion nematodes (Pratylenchus neglectus and P. thornei) with and without nematicide.Crossref | Pratylenchus neglectus and P. thornei) with and without nematicide.&journal=Australian Journal of Agricultural Research&volume=50&pages=617-622&publication_year=1999&author=SP%20Taylor&hl=en&doi=10.1071/A98103" target="_blank" rel="nofollow noopener noreferrer" class="reftools">GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1MXjslyjsLg%3D&md5=32f07b1830c3845947f173daf2867916CAS |
Thompson JP, Brennan PS, Clewett TG, Sheedy JG, Seymour NP (1999) Progress in breeding wheat for tolerance and resistance to root-lesion nematode (Pratylenchus thornei). Australasian Plant Pathology 28, 45–52.
| Progress in breeding wheat for tolerance and resistance to root-lesion nematode (Pratylenchus thornei).Crossref | Pratylenchus thornei).&journal=Australasian Plant Pathology&volume=28&pages=45-52&publication_year=1999&author=JP%20Thompson&hl=en&doi=10.1071/AP99006" target="_blank" rel="nofollow noopener noreferrer" class="reftools">GoogleScholarGoogle Scholar |
Thompson JP, Clewett TG (1986) Research on root-lesion nematode—Occurrence and wheat varietal reaction, Queensland. Queensland Wheat Research Institute, Biennial Report for 1982–84.
Thompson JP, Owen KJ, Stirling GR, Bell MJ (2008) Root-lesion nematodes (Pratylenchus thornei and P. neglectus): a review of recent progress in managing a significant pest of grain crops in northern Australia. Australasian Plant Pathology 37, 235–242.
| Root-lesion nematodes (Pratylenchus thornei and P. neglectus): a review of recent progress in managing a significant pest of grain crops in northern Australia.Crossref | Pratylenchus thornei and P. neglectus): a review of recent progress in managing a significant pest of grain crops in northern Australia.&journal=Australasian Plant Pathology&volume=37&pages=235-242&publication_year=2008&author=JP%20Thompson&hl=en&doi=10.1071/AP08021" target="_blank" rel="nofollow noopener noreferrer" class="reftools">GoogleScholarGoogle Scholar |
Vanstone VA, Hollaway GJ, Stirling GR (2008) Managing nematode pests in the southern and western regions of the Australian cereal industry: continuing progress in a challenging environment. Australasian Plant Pathology 37, 220–234.
| Managing nematode pests in the southern and western regions of the Australian cereal industry: continuing progress in a challenging environment.Crossref | GoogleScholarGoogle Scholar |
Warburton M, Crossa J, Franco J, Kazi M, Trethowan R, Rajaram S, Pfeiffer W, Zhang P, Dreisigacker S, van Ginkel M (2006) Bringing wild relatives back into the family: recovering genetic diversity in CIMMYT improved wheat germplasm. Euphytica 149, 289–301.
| Bringing wild relatives back into the family: recovering genetic diversity in CIMMYT improved wheat germplasm.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XmvVaru74%3D&md5=91777ec176d5565792f41dd6b11e1acfCAS |
Zadoks JC, Chang TT, Konzak CF (1974) A decimal code for the growth stage of cereals. Weed Research 14, 415–421.
| A decimal code for the growth stage of cereals.Crossref | GoogleScholarGoogle Scholar |