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Advances in wheat breeding techniques Alison R. Bentley and Ian Mackay, NIAB, United Kingdom 1 Introduction 2 Pedigree selection and SSD 3 Doubled haploids 4 Bulk breeding and backcross breeding 5 Advanced breeding methods: F1 hybrid breeding 6 MAS and mapping 7 Genomic selection 8 Genetic engineering, gene and genome editing 9 Mutation breeding 10 Case study: RABID 11 Summary and future trends 12 Where to look for further information 13 References

1 Introduction Although plant breeding began over 9000 years ago, modern plant breeding is based on the much more recent realization (about 300 years ago) that both crossing and selection are required to make genetic progress. Various schemes and systems to improve crop plants have been developed, or are proposed, although new tools and techniques can deliver improved wheat varieties to a farmer’s field only if they are applied within breeding programmes. This application requires the integration and application of quantitative genetics and statistics. Most agronomic traits targeted by breeding are quantitatively inherited, being controlled by many genes and strongly environmentally influenced. Both of these factors complicate the precision of selecting and producing genetically improved wheat varieties. Recent and near future technology developments and advancements offer huge potential for wheat improvement, and plant breeding will be at the heart of delivering these new gains. Although systematic plant breeding has produced the yield advances necessary to feed

http://dx.doi.org/10.19103/AS.2016.0004.05 Š Burleigh Dodds Science Publishing Limited, 2016. All rights reserved.


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Advances in wheat breeding techniques

the world’s population, the reality of securing future food security challenges the capacity of current methodologies. The breeder’s equation (Lush, 1937) is a statistical summation of the evolution of quantitative traits. It measures the change in the mean of a population over a single generation as a function of the selection differential (a measure of the difference in mean trait values between selected individuals and the entire population; Falconer and Mackay, 1996). The complexity of multi-locus inheritance (quantitative variation involving many genes) is distilled into the narrow sense heritability h2, the proportion of variation attributed to additive genetic effects. Breeding is targeted at increasing the rate of genetic gain via the components of the equation. This encompasses increasing the selection intensity (the number of individuals selected), the selection accuracy (the precision by which individuals are selected), genetic variation and reducing the years per breeding cycle. All methods of wheat breeding operate within the parameters of the breeder’s equation and new technology must be assessed within the context of increasing the rate of genetic gain. Wheat is an inbreeding species, affecting the breeding methodologies that are applied to it. There are five generally used methods of breeding: •• •• •• •• ••

pedigree selection single seed descent (SSD) doubled haploids (DH) bulk selection backcross breeding

All of these breeding methods require a priori identification of parents to enter the breeding programme. These breeding methods will be discussed in this chapter, along with other advanced breeding methods, which include the following: •• hybrid breeding •• the application of genetics (via marker-assisted breeding) and genomics (as genomic selection [GS]) •• potential uses of genetic engineering and gene editing •• mutation breeding The chapter includes a case study on rapid bulk inbreeding (RABID).

2  Pedigree selection and SSD Pedigree selection is the most common and well-established method of breeding inbred crops. It was first attributed to Nilsson-Ehle at the Svalof Institute in Sweden around 1909 (Åkerberg, 1986) and was reported in literature in 1912 (Newman, 1912) and then again in 1927 (Love, 1927) and was implemented in practice by Louis Vilmorin and F. F. Hallet during the mid-nineteenth century (Kingsbury, 2009). Inbreeding and selection occur simultaneously and rely on the breeder selecting superior individuals from genetically diverse, segregating generations. To begin, a cross is made between near homozygous parental lines and selection is made in the early generations where each plant is genetically distinct. The selfed seed from selected individuals is grown as © Burleigh Dodds Science Publishing Limited, 2016. All rights reserved.


Advances in wheat breeding techniques3

single-plant progenies and over successive selfing generations, and selection occurs between families and between plants within families. The number of selections made depends on the available resources, the expected genetic variability and the number of generations of selection (Fehr, 1991). Early generation selection is typically made on visually scorable traits including height, flowering and disease resistance. It also allows for inferior genotypes to be discarded prior to expensive evaluation. Bulked seed from each of the final-selected single-plant progeny rows/plots are progressed into yield and quality trials as potential new varieties. Although conceived in the late 1930s (Goulden, 1939), SSD came of age in the 1970s (Knott and Kumar, 1975). Goulden (1941) noted that a wheat breeding programme could be divided into two parts: first, the development of pure lines from a segregating population, and second, the selection among the pure lines for desirable characters. Decoupling inbreeding from selection (in contrast to pedigree selection) means that the development of pure lines can occur more rapidly than if it has to coincide with selection environments. Because of this, SSD is the most commonly used method for rapid generation of recombinant inbred lines (RILs) within breeding programmes. Selfing occurs over many generations (determined by the time available to the breeder) with a focus on rapid production of seed. At each selfing generation, a single seed is progressed to the next generation from each parental plant, meaning each individual is from a separate F2 individual. Following rapid inbreeding, lines are multiplied to generate seed for yield testing. Selection on a single-plant basis can be practised during any generation for traits that can be described by using single plants. Within a traditional pedigree breeding approach, the use of marker-assisted selection (MAS; described in Section 6) to select for favourable alleles will increase efficiency (Koebner and Summers, 2003), provided suitable markers are available for the selected trait. As the F2 is large, and heavy selection pressure is applied in the F2, the early use of markers can increase efficiency. In SSD, each of the derived inbred lines originates from a separate F2 individual. This reduces, but does not eliminate, the loss of genetic variation through drift during the selfing process, thus maintaining response to selection. RABID is proposed as an alternative method of SSD that allows more crosses to be progressed speculatively. It can easily incorporate selection for traits of high heritability, such as flowering time, during the bulk inbreeding process. The speeding up of the breeding cycle, which RABID allows, and the use of markers in selecting among lines within a cross may also result in simple integration into schemes of GS in inbreeding species. Later in this chapter (Section 10), we demonstrate by simulation that practical RABID schemes that phenotype an equivalent number of lines exist as in an SSD programme to give the same response to selection, provided a modest number of genetic markers are used to select a set of lines with minimized relationships. Because of reduced costs during inbreeding, crosses can be made and progressed earlier in the breeding programme, before detailed information on potential parents is available. Whole crosses can then be discarded after RILs have been created with a little loss of investment. In contrast, the commitment to several generations of SSD is not usually made until more complete information on parents is available. RABID fits well with the increased use of genetic markers for GS and MAS. It also has application in the generation of mapping populations. With the continued decrease in the cost of genotyping and increase in the cost of phenotyping, RABID is proposed as a cost-effective and genetically efficient alternative to SSD. Š Burleigh Dodds Science Publishing Limited, 2016. All rights reserved.


Advances in wheat breeding techniques