Genomic selection strategies to increase genetic gain in tea breeding programs

Tea [Camellia sinensis (L.) O. Kuntze] is mainly grown in low‐ to middle‐income countries (LMIC) and is a global commodity. Breeding programs in these countries face the challenge of increasing genetic gain because the accuracy of selecting superior genotypes is low and resources are limited. Phenotypic selection (PS) is traditionally the primary method of developing improved tea varieties and can take over 16 yr. Genomic selection (GS) can be used to improve the efficiency of tea breeding by increasing selection accuracy and shortening the generation interval and breeding cycle. Our main objective was to investigate the potential of implementing GS in tea‐breeding programs to speed up genetic progress despite the low cost of PS in LMIC. We used stochastic simulations to compare three GS‐breeding programs with a Pedigree and PS program. The PS program mimicked a practical commercial tea‐breeding program over a 40‐yr breeding period. All the GS programs achieved at least 1.65 times higher genetic gains than the PS program and 1.4 times compared with Seed‐Ped program. Seed‐GSc was the most cost‐effective strategy of implementing GS in tea‐breeding programs. It introduces GS at the seedlings stage to increase selection accuracy early in the program and reduced the generation interval to 2 yr. The Seed‐Ped program outperformed PS by 1.2 times and could be implemented where it is not possible to use GS. Our results indicate that GS could be used to improve genetic gain per unit time and cost even in cost‐constrained tea‐breeding programs

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub‐genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub‐genomes A and B using neighbor‐joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome‐wide association study found only a limited number of significant marker‐trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context‐specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet

Breeding strategies for integrating new and orphan crops in production systems

In recent decades, plant breeding has shifted toward catering for intensive monocropping based on a few staple crops. This shift has led to a reduction in biodiversity, environmentally-unsustainable agricultural practices, the increased exposure of food production to climate change risks, and nutritionally inadequate diets. More sustainable agricultural practices that promote species- and nutrient-rich crops are needed, and new and orphan crops are attractive candidates for inclusion. Many orphan crops are typically grown in diverse cropping systems with low inputs, cope well with adverse climatic conditions, and are nutrient-rich. However, they have received limited research attention and have generally not yet been intensively selected or domesticated. This thesis addresses several aspects of plant breeding research that could support new and orphan crop improvement. Chapter 1 introduces concepts essential for understanding the thesis as well as thesis objectives. The allotetraploid orphan crop finger millet Eleusine coracana is a promising crop for further cultivation due to its climate resilience and rich nutritional properties. My first results chapter (Chapter 2) presents a study of phenotypic and genomic diversity in finger millet based on 423 landrace accessions collected from major cultivation areas worldwide. The application of various statistical and bioinformatics tools, building on a recently separately published genome assembly, revealed strong population structure at both phenotypic and genomic levels, with differences at the sub-genomic level shedding light on potentially complex diversification history of the crop. Extensive phenotypic variation was found in almost all of the 13 agronomic traits analysed, while genomic diversity in landraces originating from East Africa was relatively low considering this area is the primary centre of domestication. The results of this study provide a better understanding of the crop that support context-specific breeding across major cultivation regions as well as germplasm conservation. Intercropping is a promising agricultural practice for promoting diversification that is a potential entry point for new and orphan crops, as they are traditionally adapted for diverse systems and have not yet been extensively selected for monocropping. My second results chapter (Chapter 3) develops new breeding strategies for intercropping, a topic that has been largely ignored because of the challenges with traditional phenotype-based selection (e.g., costly and budget-limited field trials). Stochastic simulations were used to test the potential utility of genomic-assisted tools, particularly genomic selection. Four intercrop breeding programs using genomic selection were simulated that produced one to three times higher genetic gain per unit cost compared to a phenotypic intercrop breeding program, depending on the simulated genetic correlation between monocrop and intercrop grain yields, and the total operating cost of the breeding program. The results of this study suggest that genomic selection could be used to revitalize intercrop breeding research embracing new and orphan crops. The use of appropriate statistical models that allow for analysis of data collected on multiple traits and multiple environments within plant breeding programs is critical for increasing genetic progress in resource-limited breeding programs for new and orphan crops. Although breeders select promising genotypes based on multiple traits measured multiple environments, current statistical approaches are typically limited to analysis of multiple environments for one trait or multiple traits for one environment. My third and final results chapter (Chapter 4) develops a new genomic selection approach for analysis of data consisting of multiple traits and multiple environments, which we call the multi-trait multi-environment factor analytic linear mixed model (MTME-FA-LMM). The MTME-FA-LMM uses a genomic relationship matrix for genotypes and a joint factor analytic model for environments and traits to appropriately model genotype × trait × environment interaction, while also allowing a different genotype × environment pattern for each trait as well as a different genotype × trait pattern for each environment. In addition, the factor analytic selection tools were extended to multiple traits to provide measures of genotype overall performance and stability for each trait, summarized across environments, to allow breeders to perform simultaneous selection of promising genotypes based on multiple traits. To demonstrate the application of the new approach, a multi-trait multi-environment trial dataset from preliminary yield trials of a finger millet breeding program is used. Overall, my thesis demonstrates how various aspects of plant breeding research, including understanding germplasm diversity, developing new breeding strategies, and developing advanced statistical approaches, can support increased genetic progress in new and orphan crops to integrate them into production. My thesis concludes by presenting opportunities and challenges for future orphan crop breeding work (Chapter 5)

Citološka analiza poganjkov japonskega in češkega dresnika med rastno sezono

Fallopia japonica and Fallopia ×bohemica are two very invasive plant species in Europe and North America. Their main mode of spread is vegetative reproduction. In spring new shoots emerge from the overwintering rhizome, grow rapidly and develop broad leaves which shade undergrowth plants. We studied cell size and starch accumulation in three stem regions at five sampling times during one growth season to determine possible differences in growth dynamics of both Fallopia species. On average F. ×bohemica had somewhat larger cells than F. japonica but the differences were not significant, except in the internodes of the middle stem region with differentiating cells. Also, cell growth dynamics of both species was similar and the only difference was detectedat the 2nd sampling when cells of F. ×bohemica were more elongated. F. ×bohemica also accumulated starch earlier in the growth season and in younger tissues than F. japonica.Japonski (Fallopia japonica) in češki dresnik (F. ×bohemica) sta v Evropi in Severni Ameriki zelo invazivni tujerodni rastlinski vrsti. Nespolno razmnoževanje je glavni način njunega razširjanja in vsako pomlad iz korenike požene brst, ki hitro zraste in razvije široke liste, ki zasenčijo podrast. V raziskavi smo preučevali velikost celic in tvorbo škrobnih zrn v treh območjih stebla pri petih vzorčenjih, ki smo jih opravili v eni rastni sezoni in tako ugotavljali morebitne razlike v dinamiki rasti pri obeh vrstah dresnika. V povprečju so bile celice češkega dresnika nekoliko večje kot celice japonskega dresnika, vendar razlike niso bile statistično značilne razen v členkih srednjega dela stebla z diferencirajočimi se celicami. Tudi dinamika celične rasti je bila podobna pri obeh vrstah dresnika razen pri 2. vzorčenju, ko so bile celice češkega dresnika bolj podaljšane. Češki dresnik je v primerjavi z japonskim kopičil škrob prej in v mlajših tkivih

Cytological analysis of Fallopia japonica and Fallopia ×bohemica shoots during growth season

Fallopia japonica and Fallopia ×bohemica are two very invasive plant species in Europe and North America. Their main mode of spread is vegetative reproduction. In spring new shoots emerge from the overwintering rhizome, grow rapidly and develop broad leaves which shade undergrowth plants. We studied cell size and starch accumulation in three stem regions at five sampling times during one growth season to determine possible differences in growth dynamics of both Fallopia species. On average F. ×bohemica had somewhat larger cells than F. japonica but the differences were not significant, except in the internodes of the middle stem region with differentiating cells. Also, cell growth dynamics of both species was similar and the only difference was detected at the 2nd sampling when cells of F. ×bohemica were more elongated. F. ×bohemica also accumulated starch earlier in the growth season and in younger tissues than F. japonica