A multi-part strategy for introgression of exotic germplasm into elite plant breeding programs using genomic selection

Some of the most economically important traits in plant breeding show highly polygenic inheritance. Genetic variation is a key determinant of the rates of genetic improvement in selective breeding programs. Rapid progress in genetic improvement comes at the cost of a rapid loss of genetic variation. Germplasm available through expired Plant Variety Protection (exPVP) lines is a potential resource of variation previously lost in elite breeding programs. Introgression for polygenic traits is challenging, as many genes have a small effect on the trait of interest. Here we propose a way to overcome these challenges with a multi-part pre-breeding program that has feedback pathways to optimise recurrent genomic selection. The multi-part breeding program consists of three components, namely a bridging component, population improvement, and product development. Parameters influencing the multi-part program were optimised with the use of a grid search. Haploblock effect and origin were investigated. Results showed that the introgression of exPVP germplasm using an optimised multi-part breeding strategy resulted in 1.53 times higher genetic gain compared to a two-part breeding program. Higher gain was achieved through reducing the performance gap between exPVP and elite germplasm and breaking down linkage drag. Both first and subsequent introgression events showed to be successful. In conclusion, the multi-part breeding strategy has a potential to improve long-term genetic gain for polygenic traits and therefore, potential to contribute to global food security.

Genetic Modification and Application in Cassava, Sweetpotato and Yams

Cassava (Manihot esculenta Crantz), sweetpotato (Ipomoea batatas) and yams (Dioscorea spp.) are important root and tuber crops grown for food, feed and various industrial applications. However, their genetic gain potentials are limited by breeding and genetic bottlenecks for improvement of many desired traits. This book chapter covers the applications and potential benefits of genetic modification in breeding selected outcrossing root and tuber crops. It assesses how improvement of selected root and tuber crops through genetic modification overcomes both the high heterozygosity and serious trait separation that occurs in conventional breeding, and contributes to timely achievement of improved target traits. It also assesses the ways genetic modification improves genetic gain in the root and tuber breeding programs, conclusions and perspectives. Conscious use of complementary techniques such as genetic modification in the root and tuber breeding programs can increase the selection gain by reducing the long breeding cycle and cost, as well as reliable exploitation of the heritable variation in the desired direction.

Selection Gain of Maize Haploid Inducers for the Tropical Savanna Environments

Lacking elite haploid inducers performing high haploid induction rate (HIR) and agronomic performance is one of fundamental factors hindering the rapid adoption of doubled haploid technology in maize hybrid breeding, especially under tropical savanna climate. Breeding haploid inducers for specific agro-ecology, thus, is indispensable yet challenging. We used temperate inducer Stock6 as genetic source for haploid induction ability and eight tropical maize genotypes as principal donors for agronomic adaptation. Three cycles of modified ear-to-row with 5% intra-family selection were applied in a population set of 78 putative haploid inducer families emphasized on agronomic performance, R1-nj anthocyanin intensity, and inducer seed set. Genetic gains, variance components, and heritability on given traits were estimated. Hierarchical clustering based on five selection criteria was performed to investigate the phenotypic diversity of putative families. Cycle effect was predominant for all observed traits. Realized genetic gain was positive for HIR (0.40% per cycle) and inducer seed set (30.10% or 47.30 seeds per ear per cycle). In this study, we reported the first haploid inducers for regions under tropical savanna climate. Three inducer families, KHI-42, KHI-54, and KHI-64, were promising as they possessed HIR about 7.8% or 14 haploid seeds per tester ear and inducer seed rate about 95.0% or 208 inducer seeds per ear. The breeding method was effective for enhancing the seed set and the expression of R1-nj anthocyanin marker of inducers, yet it showed a low effectiveness to improve haploid induction rate. Introgression of temperate inducer Stock6 into tropical gene pool followed by phenotypic selections through modified ear-to-row selection on inducer seed set and R1-nj marker did not compromise the agronomic traits of tropical inducer families. Implications and further strategies for optimizing genetic gain on HIR are discussed.

Breeding Maize for Food and Nutritional Security

Maize occupies an important position in the world economy, and serves as an important source of food and feed. Together with rice and wheat, it provides at least 30 percent of the food calories to more than 4.5 billion people in 94 developing countries. Maize production is constrained by a wide range of biotic and abiotic stresses that keep afflicting maize production and productivity causing serious yield losses which bring yield levels below the potential levels. New innovations and trends in the areas of genomics, bioinformatics, and phenomics are enabling breeders with innovative tools, resources and technologies to breed superior resilient cultivars having the ability to resist the vagaries of climate and insect pest attacks. Maize has high nutritional value but is deficient in two amino acids viz. Lysine and Tryptophan. The various micronutrients present in maize are not sufficient to meet the nutritive demands of consumers, however the development of maize hybrids and composites with modifying nutritive value have proven to be good to meet the demands of consumers. Quality protein maize (QPM) developed by breeders have higher concentrations of lysine and tryptophan as compared to normal maize. Genetic level improvement has resulted in significant genetic gain, leading to increase in maize yield mainly on farmer’s fields. Molecular tools when collaborated with conventional and traditional methodologies help in accelerating these improvement programs and are expected to enhance genetic gains and impact on marginal farmer’s field. Genomic tools enable genetic dissections of complex QTL traits and promote an understanding of the physiological basis of key agronomic and stress adaptive and resistance traits. Marker-aided selection and genome-wide selection schemes are being implemented to accelerate genetic gain relating to yield, resilience, and nutritional quality. Efforts are being done worldwide by plant breeders to develop hybrids and composites of maize with high nutritive value to feed the people in future.

Evidence for the Application of Emerging Technologies to Accelerate Crop Improvement – A Collaborative Pipeline to Introgress Herbicide Tolerance Into Chickpea

Accelerating genetic gain in crop improvement is required to ensure improved yield and yield stability under increasingly challenging climatic conditions. This case study demonstrates the effective confluence of innovative breeding technologies within a collaborative breeding framework to develop and rapidly introgress imidazolinone Group 2 herbicide tolerance into an adapted Australian chickpea genetic background. A well-adapted, high-yielding desi cultivar PBA HatTrick was treated with ethyl methanesulfonate to generate mutations in the ACETOHYDROXYACID SYNTHASE 1 (CaAHAS1) gene. After 2 years of field screening with imidazolinone herbicide across >20 ha and controlled environment progeny screening, two selections were identified which exhibited putative herbicide tolerance. Both selections contained the same single amino acid substitution, from alanine to valine at position 205 (A205V) in the AHAS1 protein, and KASP™ markers were developed to discriminate between tolerant and intolerant genotypes. A pipeline combining conventional crossing and F2 production with accelerated single seed descent from F2:4 and marker-assisted selection at F2 rapidly introgressed the herbicide tolerance trait from one of the mutant selections, D15PAHI002, into PBA Seamer, a desi cultivar adapted to Australian cropping areas. Field evaluation of the derivatives of the D15PAHI002 × PBA Seamer cross was analyzed using a factor analytic mixed model statistical approach designed to accommodate low seed numbers resulting from accelerated single seed descent. To further accelerate trait introgression, field evaluation trials were undertaken concurrent with crop safety testing trials. In 2020, 4 years after the initial cross, an advanced line selection CBA2061, bearing acetohydroxyacid synthase (AHAS) inhibitor tolerance and agronomic and disease resistance traits comparable to parent PBA Seamer, was entered into Australian National Variety Trials as a precursor to cultivar registration. The combination of cross-institutional collaboration and the application of novel pre-breeding platforms and statistical technologies facilitated a 3-year saving compared to a traditional breeding approach. This breeding pipeline can be used as a model to accelerate genetic gain in other self-pollinating species, particularly food legumes.

Simulation of pedigree vs. fully-informative marker based relationships matrices in a loblolly pine breeding population

Computer simulations of breeding strategies are an essential resource for tree breeders because they allow exploratory analyses into potential long-term impacts on genetic gain and inbreeding consequences without bearing the cost, time, or resource requirements of field experiments. Previous work has modeled the potential long-term implications on inbreeding and genetic gain using random mating and phenotypic selection. Reduction in sequencing costs has enabled the use of DNA marker-based relationship matrices in addition to or in place of pedigree-based allele sharing estimates; this has been shown to provide a significant increase in the accuracy of progeny breeding value prediction. A potential pitfall of genomic selection using genetic relationship matrices is increased coancestry among selections, leading to the accumulation of deleterious alleles and inbreeding depression. We used simulation to compare the relative genetic gain and risk of inbreeding depression within a breeding program similar to loblolly pine, utilizing pedigree-based or marker-based relationships over ten generations. We saw a faster rate of purging deleterious alleles when using a genomic relationship matrix based on markers that track identity-by-descent of segments of the genome. Additionally, we observed an increase in the rate of genetic gain when using a genomic relationship matrix instead of a pedigree-based relationship matrix. While the genetic variance of populations decreased more rapidly when using genomic-based relationship matrices as opposed to pedigree-based, there appeared to be no long-term consequences on the accumulation of deleterious alleles within the simulated breeding strategy.