13.1 Sustainable Increase in Global Wheat Production

Wheat (Triticum spp.) is a major source of carbohydrates and is used as a staple food for global inhabitants. Genetically, diverse wheat resources show variable ploidy level (diploid, tetraploid, and hexaploid) as a result of prolonged evolution and the wheat domestication process (Jordan et al. 2015). As an allopolyploid crop, wheat breeding and genetics investigations are generally considered challenging and has provided for conventional breeding approaches to be complemented by genome-assisted breeding including the genomics toolbox with the available reference genomes to deal with the highly repetitive wheat genome and to decipher genotype–phenotype associations (Varshney et al. 2021a). More specifically, the increased sophistication of sequencing technologies/interpretation has led to extensive re-sequencing of low-copy genomic regions (Nyine et al. 2019) in diverse wheat haplotype mapping populations that are managed with reduced crop-cycle through speed breeding, or fast-forward breeding, toward the wheat improvement (Varshney et al. 2021b; Jordan et al. 2022). A key requirement is to understand diverse wheat genetic resources for trait improvement, environmental adaptations, and disease resistance under ongoing climate changing scenario.

Genomics-assisted breeding (GAB) has contributed to the enhancement of germplasm and the crop/cultivar development process to characterize allelic variation for important agronomic traits associated with crop production and quality attributes as well as tolerance to abiotic and biotic stresses (Varshney et al. 2005). With the advent of genome sequencing and the inclusion of genetic-based markers in sequencing repositories, a variety of genomic tools and approaches have become accessible for use in plant breeding. These methods and techniques include GAB which is capable of assisting growers in selecting appropriate parental lines for various crossing programs in the breeding platform, which will ultimately result in the creation of genetic variation for pyramiding into breeding lines (Varshney et al. 2005). A significant variety of molecular genetic markers, such as simple sequence repeat (SSR), diversity array technology (DArT), single feature polymorphism (SFP), and single nucleotide polymorphisms (SNP), are now available, as well as inter-specific and intra-specific mapping populations (Kover et al. 2009) for chromosome sequence-aided molecular markers-based selection strategies (Akpinar et al. 2017; Maccaferri et al. 2022).

13.2 Application of Genomic Breeding (GB) to the Development of Future Crops

Several GB methods, including marker-assisted selection (MAS), marker-assisted recurrent selection (MARS), haplotype-based breeding (HBB), marker-assisted backcrossing (MABC), promotion/removal of allele through genome editing (PAGE/RAGE), and genomic selection (GS), can be used in concurrently with speed breeding to design new varieties of crops (Varshney et al. 2021a).

13.2.1 Haplotype-Based Breeding (HBB) in Wheat

Recent developments in crop genomics have sparked the development of novel technologies that aim for diversifying the procedures of plant propagative strategies by combining desired phenotypes (Fig. 13.1) with the method of haplotype construction developed using information from sequencing genotypes (Varshney et al. 2005, 2021a). Aiming for haplotype construction, various crop species have made use of large SNP data sets obtained from genomic sequence-based technologies on multiple genotypes (Varshney et al. 2005) in order to define haplotype-linked biomarkers. Haplotype construction was initially challenging for the short-read sequences obtained through the second-generation sequencing because of the lower probability of the presence of allelic variations in the form of single nucleotide polymorphism (SNP) or insertion-deletions (InDel). In contrast, the definition of haplotypes using long-read sequences has become simpler, and in many specific crop species, the information is readily available from a large number of different individuals, including using single-cell approaches, and Pacific Biosciences (PacBio) and/or Oxford Nanopore Technology (ONT) based high-quality long-read sequencing technologies that show considerably greater genomic diversity (Torkamaneh and Belzile 2022). The method for constructing haplotypes using the breeding line sequencing data proceeds with the discovery and evaluation of the changes in the haplotype fingerprint using whole genome sequencing (WGS) data (Bevan et al. 2017; Bhat et al. 2021). Constructing haplotypes between adjacent SNPs on a chromosome is an alternate method that may be used to increase the genome-wide association study (GWAS) potential. Haplotypes, in this way, are particular collections of alleles that are detected on a single chromosome. They are passing throughout the generation of the population collectively, and there is a low possibility that they may recombine in the future.

Fig. 13.1
figure 1

Overview of breeding strategies for crop improvement through GAB. The image was created using BioRender (https://biorender.com/)

Research on Triticum spp. has evinced that GWAS investigation based on haplotypes can be preferable to analysis based on a single marker in assessing the impacts of allelic variation (Sehgal et al. 2020) and allows HBB to produce a customized crop varieties by combining better haplotypes into a single plant, particularly novel combinational haplogroups. A wider pool of haplotype-linked genetic markers provides wheat breeders with a greater chance of developing high-performing, linkage-drag-free hybrids (Varshney et al. 2021b). The transmission of haplotypes within genetic populations must be monitored in order to pinpoint the best possible parents to cross and produce offspring with the beneficial adaptive and desired traits that are crucial for trying to create novel genetic compositions. Based on this premise, useful haplotypes have been identified by incorporating the combined results of extensive, entire, genome sequencing, and haplo-phenotyping database analysis (Bhat et al. 2021).

The construction of haplotype blocks typically makes use of the following three methods in order: (1) user-defined length, (2) sliding window, and (3) linkage disequilibrium (LD). The user-defined set length of haplotype blocks (2–15 bp) is the simplest way; however, the created haplotypes do not represent genomic factors such as crossover or LD (Sehgal et al. 2020), nor do they represent a common evolutionary process (Templeton et al. 2004). The second one is by far the most popular choice among GWAS researchers when it comes to the construction of haplotypes (Sehgal et al. 2020). This method is simple and straightforward to use; but, when neighboring SNPs are strongly linked to each other, it produces information that is redundant; hence, it is no-more helpful than using SNPs alone (Sehgal et al. 2020). It is challenging to determine the optimal window size for a genome-wide scan when LD frequencies differ throughout large genetic variants (Sehgal et al. 2020). This is similar to the previous point. In terms of finding instances of past integration in the population of interest, the LD-aided approach stands out as being the most effective (Qian et al. 2017; Sehgal et al. 2020).

According to an investigation by Brinton et al. (2020) on haplotype blocks in wheat, seven haplotypes (namely H1, H2,….,H7) were identified that included the gene TaGW2-A in the highly conserved genetic regions of chromosome 6A responsible for increased yield characteristics. As the two SNP markers based on the promoter regions of this gene could not discriminate the haplo-blocks, the haplotype block provided more gene-associated markers for complete reliability (Varshney et al. 2021b). Studies by Luján Basile et al. (2019) characterized haplotype blocks and GWAS in Argentinian bread wheats using genetic molecular markers and SNP profiling and revealed that several haplotype blocks span throughout the genome and including conserved genetic regions, e.g., 1BL/1RS wheat/rye translocation site on chromosome 1BS (e.g., in Chinese wheats; see Ru et al. 2020). Moreover, most of the haplotypes identified had significant effects on the yield attributes through multi-locational breeding trials. For spring wheat genetic resources, an approach of haplotype-based GWAS was targeted for epistatic interactions of multi-locational breeding trials in CIMMYT (Mexico) led by Sehgal et al. (2020). This study aimed to explore the stable genomic regions of the haplotypes for improved yield components and haplotype interactions and used LD approaches as numerous haplotype blocks were designed to span through >14 Mb of wheat genome. Haplotype-based GWAS revealed stable associations under drought stress environments with chromosomal hotspots. These studies support the need for developing genetic markers, and their deployment in agricultural crop development that are reliant on haplotypes rather than just single SNPs. Because full-genome sequencing data for the breeding lines collection in a variety of crops is expanding, it can be anticipated that the HBB method will continue to be used in the years to come (Varshney et al. 2021a).

Figure 13.1 provides a description of the integrative techniques that can be used to either add beneficial allelic variants to wheat genetic resources or remove harmful allelic variants from them in order to prepare future crop breeding techniques. The collections of germplasm that are stored in gene banks include both advantageous and detrimental impact alleles. Combining high-throughput sequencing with multi-omics assays and field phenotyping offers a valuable tool for connecting genomic variants with key phenotypes. The acquisition of knowledge about the genes that are responsible for important plant characteristics lays the path for haplotype-based genetic breeding or de novo domestication (Qian et al. 2017; Bhat et al. 2021; Varshney et al. 2021b). In this regard, speed breeding (SB) or fast-forward breeding approach will contribute to the acceleration of the advances made in crop breeding pipelines. The HBB strategy requires monitoring haplotype transfer via breeding lineages as a crucial step in creating novel genomic variants because it helps select the appropriate parents for breeding to create offspring with the desired traits. Incorporating genomic information into defining recombinants formed by mating distinct sets of parents can help simplify desired traits of interest, in particular for complex traits such as adaptation to harsh environments (Jensen et al. 2020) where it is necessary to distinguish between a correlation between different traits that are attributable to genuine linkage among the genes, or due to the pleiotropic actions of a given set of genes (Bhat et al. 2021; Dixon et al. 2020). In the case of crops whose genomes include extensive linkage disequilibrium (LD) blocks, an HBB method becomes more pertinent since the LD blocks can be regions of conserved genetic variation.

13.2.2 Involvement of Speed Breeding in Haplotype Mapping for Wheat Genetic Resources

In plant breeding, generation time of a crop is a major factor to stabilize homozygote lines with enhanced genetic gain through hybridization and conventional breeding schemes. Some approaches such as double haploid, shuttle breeding, and tissue culture of embryo can help to minimize the generation time (Bhat et al. 2021). But to some extent, major key crops are intractable in double haploid techniques. Moreover, genetic linkages, recombination, and the lacuna of dedicated plant organ and tissue cultural infrastructure promote additional breeding avenues to fixing the genes. The development of a new and more sophisticated breeding method known as speed (fast) breeding (SB) has made it feasible to hasten agricultural innovation by shortening plant phenological cycle and gear up the progression of generational advancement (Ghosh et al. 2018; Watson et al. 2018). Speed or fast-forward breeding program deployed in several ways, such as by expanding light exposure time to the given crop species, instantaneously after it becomes available for grain harvesting, for fast propagation reduces the amount of time it takes for certain day-neutral and/or long-day plants to produce new generations (Ghosh et al. 2018; Watson et al. 2018). The basic fact in wheat SB is utilizing the early flowering period by manipulating the photoperiod (day length) and temperature (vernalization or cold requirement) under controlled condition (Ghosh et al. 2018). In this way, haplotypes and improved new varieties belonging to the same species can be developed through the synchronizing flowering time (anthesis) and introgressed into marker-assisted molecular breeding program coupled with abiotic stress tolerance (Song et al. 2022; Gahlaut et al. 2023). Under SB conditions, it could be possible to meet the flowering time of both wheat parents involved in the crossing experiments and propagation of future generations in very short time and space manner. Moreover, such accelerated generation times of this polyploid crop enable phenotypic screening of transformants for further selection and marker-aided investigation to improve grain yield, nutritional quality, improving beneficial traits, flowering time as well as adaptations to both environmental instabilities and disease pressures (Watson et al. 2018). Along with the screening of the wheat lines for abiotic and biotic stress response, SB protocols and techniques can be manipulated for rapid screening of the population even in the off season with the screening being done early in the life cycle of the plant generations (Alahmad et al. 2018; Ghosh et al. 2018). This is advantageous for breeding procedures especially for pyramiding beneficial/resistance genes for the production of climate-smart wheat. Speed breeding acts as a bridge to utilizing superior haplotype with exotic and adaptive alleles for haplotype-based breeding (HBB), genomic selection (GS), and genome editing. Using the SB approaches, accelerated generation can deliver the improved variety after going through high-throughput phenotyping, marker-assisted selection (MAS), genotyping, and sequencing (Fig. 13.2). In polyploid crops, haplotype phasing and scaffolding are becoming more advantageous as a result of increased chromosomal configuration monitoring (Zhang et al. 2019), sequencing, and Bionano Genomics (BNG) optical mapping-based genomic assemblies. SB coupled with single seed descent (SSD) for generation advancement of haplotypes and other bi- and/or multi-parental breeding populations enhances molecular marker-aided breeding (MAB) and precise genome editing for the desired trait(s).

Fig. 13.2
figure 2

Involvement of speed breeding in haplotype mapping to generate improved variety. This figure was prepared using BioRender application (https://biorender.com/)

13.3 Conclusion and Future Perspective

Breeding, especially breeding of main crops such as wheat, is as old as human history, and the focus on selection for mainly yield and high quality has tended to restrict the genetic diversity of modern wheat. The region in which domesticated wheat originated, namely in Mesopotamia in the Harran region of Turkey, has however a very large gene pool of Triticeae species with characteristics that provide for growth under challenging environmental conditions as well as to coping with multiple biotic factors. As detailed in Chap. 12, it is clear that these valuable abilities can be recovered in domesticated wheat varieties through alien introgression. For the present chapter, we have argued that molecular technologies can be captured in the form of haplotype mapping combining selection based on haplotype signatures with speed breeding approaches as a primary genomics-assisted breeding strategy for complex traits.