Testcross performance of doubled haploid lines from European flint maize landraces is promising for broadening the genetic base of elite germplasm

Paclitaxel and Caffeine-Taurine, New Colchicine Alternatives for Chromosomes Doubling in Maize Haploid Breeding

The doubled haploid (DH) technology is employed worldwide in various crop-breeding programs, especially maize. Still, restoring tassel fertility is measured as one of the major restrictive factors in producing DH lines. Colchicine, nitrous oxide, oryzalin, and amiprophosmethyl are common chromosome-doubling agents that aid in developing viable diploids (2n) from sterile haploids (n). Although colchicine is the most widely used polyploidy-inducing agent, it is highly toxic to mammals and plants. Therefore, there is a dire need to explore natural, non-toxic, or low-toxic cheaper and accessible substitutes with a higher survival and fertility rate. To the best of our knowledge, the advanced usage of human anticancer drugs "Paclitaxel (PTX)" and "Caffeine-Taurine (CAF-T)" for in vivo maize haploids doubling is being disclosed for the first time. These two antimitotic and antimicrotubular agents (PTX and CAF-T) were assessed under various treatment conditions compared to colchicine. As a result, the maximum actual doubling rates (ADR) for PTX versus colchicine in maize haploid seedlings were 42.1% (400 M, 16 h treatment) versus 31.9% (0.5 mM, 24 h treatment), respectively. In addition, the ADR in maize haploid seeds were CAF-T 20.0% (caffeine 2 g/L + taurine 12 g/L, 16 h), PTX 19.9% (100 μM, 24 h treatment), and colchicine 26.0% (2.0 mM, 8 h treatment). Moreover, the morphological and physiological by-effects in haploid plants by PTX were significantly lower than colchicine. Hence, PTX and CAF-T are better alternatives than the widely used traditional colchicine to improve chromosome-doubling in maize crop.

Genomic prediction in hybrid breeding: I. Optimizing the training set design

Training sets produced by maximizing the number of parent lines, each involved in one cross, had the highest prediction accuracy for H0 hybrids, but lowest for H1 and H2 hybrids. Genomic prediction holds great promise for hybrid breeding but optimum composition of the training set (TS) as determined by the number of parents (nTS) and crosses per parent (c) has received little attention. Our objective was to examine prediction accuracy ([Formula: see text]) of GCA for lines used as parents of the TS (I1 lines) or not (I0 lines), and H0, H1 and H2 hybrids, comprising crosses of type I0 × I0, I1 × I0 and I1 × I1, respectively, as function of nTS and c. In the theory, we developed estimates for [Formula: see text] of GBLUPs for hybrids: (i)[Formula: see text] based on the expected prediction accuracy, and (ii) [Formula: see text] based on [Formula: see text] of GBLUPs of GCA and SCA effects. In the simulation part, hybrid populations were generated using molecular data from two experimental maize data sets. Additive and dominance effects of QTL borrowed from literature were used to simulate six scenarios of traits differing in the proportion (τSCA = 1%, 6%, 22%) of SCA variance in σG2 and heritability (h2 = 0.4, 0.8). Values of [Formula: see text] and [Formula: see text] closely agreed with [Formula: see text] for hybrids. For given size NTS = nTS × c of TS, [Formula: see text] of H0 hybrids and GCA of I0 lines was highest for c = 1. Conversely, for GCA of I1 lines and H1 and H2 hybrids, c = 1 yielded lowest [Formula: see text] with concordant results across all scenarios for both data sets. In view of these opposite trends, the optimum choice of c for maximizing selection response across all types of hybrids depends on the size and resources of the breeding program.

Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties

Landraces, that is, traditional varieties, have a large diversity that is underexploited in modern breeding. A novel DNA pooling strategy was implemented to identify promising landraces and genomic regions to enlarge the genetic diversity of modern varieties. As proof of concept, DNA pools from 156 American and European maize landraces representing 2340 individuals were genotyped with an SNP array to assess their genome-wide diversity. They were compared to elite cultivars produced across the 20th century, represented by 327 inbred lines. Detection of selective footprints between landraces of different geographic origin identified genes involved in environmental adaptation (flowering times, growth) and tolerance to abiotic and biotic stress (drought, cold, salinity). Promising landraces were identified by developing two novel indicators that estimate their contribution to the genome of inbred lines: (i) a modified Roger's distance standardized by gene diversity and (ii) the assignation of lines to landraces using supervised analysis. It showed that most landraces do not have closely related lines and that only 10 landraces, including famous landraces as Reid's Yellow Dent, Lancaster Surecrop and Lacaune, cumulated half of the total contribution to inbred lines. Comparison of ancestral lines directly derived from landraces with lines from more advanced breeding cycles showed a decrease in the number of landraces with a large contribution. New inbred lines derived from landraces with limited contributions enriched more the haplotype diversity of reference inbred lines than those with a high contribution. Our approach opens an avenue for the identification of promising landraces for pre-breeding.

Androgenesis-Based Doubled Haploidy: Past, Present, and Future Perspectives

Androgenesis, which entails cell fate redirection within the microgametophyte, is employed widely for genetic gain in plant breeding programs. Moreover, androgenesis-responsive species provide tractable systems for studying cell cycle regulation, meiotic recombination, and apozygotic embryogenesis within plant cells. Past research on androgenesis has focused on protocol development with emphasis on temperature pretreatments of donor plants or floral buds, and tissue culture optimization because androgenesis has different nutritional requirements than somatic embryogenesis. Protocol development for new species and genotypes within responsive species continues to the present day, but slowly. There is more focus presently on understanding how protocols work in order to extend them to additional genotypes and species. Transcriptomic and epigenetic analyses of induced microspores have revealed some of the cellular and molecular responses required for or associated with androgenesis. For example, microRNAs appear to regulate early microspore responses to external stimuli; trichostatin-A, a histone deacetylase inhibitor, acts as an epigenetic additive; ά-phytosulfokine, a five amino acid sulfated peptide, promotes androgenesis in some species. Additionally, present work on gene transfer and genome editing in microspores suggest that future endeavors will likely incorporate greater precision with the genetic composition of microspores used in doubled haploid breeding, thus likely to realize a greater impact on crop improvement. In this review, we evaluate basic breeding applications of androgenesis, explore the utility of genomics and gene editing technologies for protocol development, and provide considerations to overcome genotype specificity and morphogenic recalcitrance in non-model plant systems.

Diversity Assessment of the Montenegrin Maize Landrace Gene Pool Maintained in Two Gene Banks

Due to the loss of agro-biodiversity, there is a strong effort to find apparent and efficient mechanisms for the conservation and sustainable use of genetic diversity. A joint monitoring of the diversity and collections structure of the Montenegrin maize landraces conserved in the Serbian (MRIZPGB) and Montenegrin (MGB) gene banks has been conducted in order to improve the composition of the collections and to identify and eliminate possible redundancy. Based on a separate analysis of white- and yellow-orange maize landraces, it can be concluded that the diversity and evolution of distinct maize landraces grown and collected in Montenegro have been simultaneously shaped by both environmental (i.e., natural selection) and socially driven factors (farmers’ selection, migration and colonization processes of the human population). Although it has been determined that the authenticity and variability of the Montenegrin maize landraces gene pool have largely been preserved in the MRIZPGB collection, a significant amount of redundancy was observed. The obtained results will contribute to the cost-efficient conservation of the maize gene pool in the Montenegrin and Serbian gene banks. The recognized and well-preserved original variability of the MRIZPGB and MGB Montenegrin gene pool represents a valuable source for pre-breeding activities on broadening the white and flint maize breeding programmes under temperate conditions.

Genetic diversity and selection signatures in maize landraces compared across 50 years of in situ and ex situ conservation

Genomics-based, longitudinal comparisons between ex situ and in situ agrobiodiversity conservation strategies can contribute to a better understanding of their underlying effects. However, landrace designations, ambiguous common names, and gaps in sampling information complicate the identification of matching ex situ and in situ seed lots. Here we report a 50-year longitudinal comparison of the genetic diversity of a set of 13 accessions from the state of Morelos, Mexico, conserved ex situ since 1967 and retrieved in situ from the same donor families in 2017. We interviewed farmer families who donated in situ landraces to understand their germplasm selection criteria. Samples were genotyped by sequencing, producing 74,739 SNPs. Comparing the two sample groups, we show that ex situ and in situ genome-wide diversity was similar. In situ samples had 3.1% fewer SNPs and lower pairwise genetic distances (F_st 0.008-0.113) than ex situ samples (F_st 0.031-0.128), but displayed the same heterozygosity. Despite genome-wide similarities across samples, we could identify several loci under selection when comparing in situ and ex situ seed lots, suggesting ongoing evolution in farmer fields. Eight loci in chromosomes 3, 5, 6, and 10 showed evidence of selection in situ that could be related with farmers' selection criteria surveyed with focus groups and interviews at the sampling site in 2017, including wider kernels and larger ear size. Our results have implications for ex situ collection resampling strategies and the in situ conservation of threatened landraces.

Heterosis and Hybrid Crop Breeding: A Multidisciplinary Review

Although hybrid crop varieties are among the most popular agricultural innovations, the rationale for hybrid crop breeding is sometimes misunderstood. Hybrid breeding is slower and more resource-intensive than inbred breeding, but it allows systematic improvement of a population by recurrent selection and exploitation of heterosis simultaneously. Inbred parental lines can identically reproduce both themselves and their F1 progeny indefinitely, whereas outbred lines cannot, so uniform outbred lines must be bred indirectly through their inbred parents to harness heterosis. Heterosis is an expected consequence of whole-genome non-additive effects at the population level over evolutionary time. Understanding heterosis from the perspective of molecular genetic mechanisms alone may be elusive, because heterosis is likely an emergent property of populations. Hybrid breeding is a process of recurrent population improvement to maximize hybrid performance. Hybrid breeding is not maximization of heterosis per se, nor testing random combinations of individuals to find an exceptional hybrid, nor using heterosis in place of population improvement. Though there are methods to harness heterosis other than hybrid breeding, such as use of open-pollinated varieties or clonal propagation, they are not currently suitable for all crops or production environments. The use of genomic selection can decrease cycle time and costs in hybrid breeding, particularly by rapidly establishing heterotic pools, reducing testcrossing, and limiting the loss of genetic variance. Open questions in optimal use of genomic selection in hybrid crop breeding programs remain, such as how to choose founders of heterotic pools, the importance of dominance effects in genomic prediction, the necessary frequency of updating the training set with phenotypic information, and how to maintain genetic variance and prevent fixation of deleterious alleles.

Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger's genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.

Using Metabolomics to Assist Plant Breeding

Recent methodological advances in both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) have provided a deep understanding of metabolic regulation occurring in plant cells. The application of these techniques to agricultural systems is, however, subject to more complex interactions. Here we summarize a step-by-step modern metabolomics methodology that generates metabolome data toward the implementation of metabolomics in crop breeding. We describe a metabolic workflow, and provide guidelines for handling large sample numbers for the specific purpose of metabolic quantitative trait loci approaches.

Tracing Real-Time Transnational Hydrologic Sensitivity and Crop Irrigation in the Upper Rhine Area over the Exceptional Drought Episode 2018–2020 Using Open Source Sentinel-2 Data

Climate and regional land-use and landcover change (LUCC) impact the ecosystem of the Upper Rhine Area (URA) and transform large parts of the landscape into strongly irrigated agricultural cropland. The increase of long-term drought periods and the trend towards low summer precipitation totals trigger an increase in groundwater scarcity and amplify the negative effects of extensive irrigation purposes and freshwater consumption in a hydrologically sensitive region in Central Europe. This article presents qualitative transnational open source remote sensing temporal series of vegetation indices (NDVI) and groundwater level development to tracing near real-time vegetation change and socio-ecological feedbacks during periods of climate extremes in the Upper Rhine Area (2018–2020). Increased freshwater consumption caused a dramatic drop in groundwater availability, which eventually led to a strong degradation of the vegetation canopy and caused governmental regulations in July 2020. Assessing vegetation growth behavior and linking groundwater reactions in the URA through open source satellite data contributes to a rapidly accessible understanding of the ecosystem’s feedbacks on the local to the transnational scale and further enables risk management and eco-political regulations in current and future decision-making processes.

Genomic prediction with a maize collaborative panel: identification of genetic resources to enrich elite breeding programs

Collaborative diversity panels and genomic prediction seem relevant to identify and harness genetic resources for polygenic trait-specific enrichment of elite germplasms. In plant breeding, genetic diversity is important to maintain the pace of genetic gain and the ability to respond to new challenges in a context of climatic and social expectation changes. Many genetic resources are accessible to breeders but cannot all be considered for broadening the genetic diversity of elite germplasm. This study presents the use of genomic predictions trained on a collaborative diversity panel, which assembles genetic resources and elite lines, to identify resources to enrich an elite germplasm. A maize collaborative panel (386 lines) was considered to estimate genome-wide marker effects. Relevant predictive abilities (0.40-0.55) were observed on a large population of private elite materials, which supported the interest of such a collaborative panel for diversity management perspectives. Grain-yield estimated marker effects were used to select a donor that best complements an elite recipient at individual loci or haplotype segments, or that is expected to give the best-performing progeny with the elite. Among existing and new criteria that were compared, some gave more weight to the donor-elite complementarity than to the donor value, and appeared more adapted to long-term objective. We extended this approach to the selection of a set of donors complementing an elite population. We defined a crossing plan between identified donors and elite recipients. Our results illustrated how collaborative projects based on diversity panels including both public resources and elite germplasm can contribute to a better characterization of genetic resources in view of their use to enrich elite germplasm.

Doubled haploid technology for line development in maize: technical advances and prospects

KEY MESSAGE

Increased efficiencies achieved in different steps of DH line production offer greater benefits to maize breeding programs. Doubled haploid (DH) technology has become an integral part of many commercial maize breeding programs as DH lines offer several economic, logistic and genetic benefits over conventional inbred lines. Further, new advances in DH technology continue to improve the efficiency of DH line development and fuel its increased adoption in breeding programs worldwide. The established method for maize DH production covered in this review involves in vivo induction of maternal haploids by a male haploid inducer genotype, identification of haploids from diploids at the seed or seedling stage, chromosome doubling of haploid (D0) seedlings and finally, selfing of fertile D0 plants. Development of haploid inducers with high haploid induction rates and adaptation to different target environments have facilitated increased adoption of DH technology in the tropics. New marker systems for haploid identification, such as the red root marker and high oil marker, are being increasingly integrated into new haploid inducers and have the potential to make DH technology accessible in germplasm such as some Flint, landrace, or tropical material, where the standard R1-nj marker is inhibited. Automation holds great promise to further reduce the cost and time in haploid identification. Increasing success rates in chromosome doubling protocols and/or reducing environmental and human toxicity of chromosome doubling protocols, including research on genetic improvement in spontaneous chromosome doubling, have the potential to greatly reduce the production costs per DH line.

European maize landraces made accessible for plant breeding and genome-based studies

KEY MESSAGE

Doubled-haploid libraries from landraces capture native genetic diversity for a multitude of quantitative traits and make it accessible for breeding and genome-based studies. Maize landraces comprise large allelic diversity. We created doubled-haploid (DH) libraries from three European flint maize landraces and characterized them with respect to their molecular diversity, population structure, trait means, variances, and trait correlations. In total, 899 DH lines were evaluated using high-quality genotypic and multi-environment phenotypic data from up to 11 environments. The DH lines covered 95% of the molecular variation present in 35 landraces of an earlier study and represent the original three landrace populations in an unbiased manner. A comprehensive analysis of the target trait plant development at early growth stages as well as other important agronomic traits revealed large genetic variation for line per se and testcross performance. The majority of the 378 DH lines evaluated as testcrosses outperformed the commercial hybrids for early development. For total biomass yield, we observed a yield gap of 15% between mean testcross yield of the commercial hybrids and mean testcross yield of the DH lines. The DH lines also exhibited genetic variation for undesirable traits like root lodging and tillering, but correlations with target traits early development and yield were low or nonsignificant. The presented diversity atlas is a valuable, publicly available resource for genome-based studies to identify novel trait variation and evaluate the prospects of genomic prediction in landrace-derived material.