Clonal Crops Research Articles

Insight into a two‐part plant breeding scheme through Bayesian optimization of budget allocations

AbstractThe total budget of a breeding program must be divided across its different parts to maximize gain. How to optimize budget allocations for a two‐part strategy breeding scheme is an unsolved problem. We used Bayesian optimization coupled with stochastic simulations of breeding schemes to determine budget allocations that maximized gain. The breeding schemes focused on a clonal crop and included a population improvement cycle (PIC) allowing one or two breeding cycles per year leading to phenotypic evaluations in a variety development pipeline (VDP) with three stages. The gain was maximized at target years 6 or 12 after initiation of genomic selection. The breeding scheme was simulated using the AlphaSimR package. Bayesian optimization was implemented using the BoTorch module of Python to optimize budget allocations to the PIC and each stage of the VDP. Allocations to the last stage of the VDP were small because information from that stage was relatively ineffective at improving genomic prediction accuracy. An unexpected interaction between the number of PIC cycles and the target year for gain affected the budget of the PIC and could be explained by conflicting needs to increase gain in the VDP or increase genomic prediction accuracy. Divergent budget allocations could generate selection gains close to the maximum, indicating some leeway in the design of breeding schemes. Simple rules of thumb for heuristic optimization did not emerge, suggesting that breeders will need to rely on simulation coupled to optimization.

Cassava Brown Streak Disease in Zambia: An Integrated Approach to Managing an Invasive Viral Disease of a Clonal Crop

Cassava Brown Streak Disease in Zambia: An Integrated Approach to Managing an Invasive Viral Disease of a Clonal Crop

Maintenance and expansion of genetic and trait variation following domestication in a clonal crop.

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterize the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and a principal starch staple for 20 million Ethiopians. Wild enset reproduction occurs strictly by sexual outcrossing, but for cultivation, it is propagated clonally and associated with diversification and specialization into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested an accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by the amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages, we found a significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. The development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.

Gene × gene and genotype × environment interactions in wheat

AbstractAccelerating the rate of genetic gain of major crops is required to meet the projected global demand for food. Genomic selection (GS) has made valuable contributions to the genetic progress of different species and is currently a routine procedure in most wheat (Triticum aestivum L.) breeding programs (WBP). Accounting for gene × gene (G × G) and genotype × environment interactions (G × E) in GS can significantly enhance genetic improvement by increasing the rate of genetic gain and adaptation of wheat cultivars. However, a comprehensive and updated knowledge of G × G and G × E methodologies is required to define the appropriate breeding strategy. In this review, we start by briefly describing the current situation and relevance of wheat breeding, then we focus on the central concepts of G × G and G × E and discuss the implications, challenges, and opportunities for the implementation of interactions in GS and wheat breeding. This review is primarily intended to be a reference material for wheat breeders and researchers. Nevertheless, most of the concepts exposed are transferable to any other autogamous or clonal crops, and are therefore useful in a much broader scope. We expect to encourage and facilitate the implementation of GS models accounting for interactions in plant breeding.

High-Density Linkage Map Constructed from a Skim Sequenced Diploid Potato Population Reveals Transmission Distortion and QTLs for Tuber Yield and Pollen Shed

The reinvention of potato, from a tetraploid clonal crop into a diploid seed-based hybrid crop, requires insight in the mutational load, recombination landscape, and the genetic basis of fertility. Genomics-based breeding and QTL discovery rely on efficient genotyping strategies such as skim sequencing, to gather genotypic information. The application of skim sequencing to full-sib population of non-inbred parents remains challenging. Here, we report on an R implementation of the OutcrossSeq pipeline for diploids. We applied this pipeline to a large diploid skim sequenced potato population. We used the resulting bin-markers for the construction of high-density parent specific linkage maps, highlighting variation in parental recombination rate and structural variations. We subsequently explored transmission ratio distortion and non-independent assortment of alleles, indicative of large-effect deleterious mutations. Finally, we identified QTLs for seedling tuber yield in pots and pollen shed. This study showcases the range of genetic analyses, from marker inference, identification of transmission ratio distortion, and linkage map construction to QTL mapping, resulting in new insights that contribute to breeding diploid potato.

The world's largest potato cryobank at the International Potato Center (CIP) - Status quo, protocol improvement through large-scale experiments and long-term viability monitoring.

Long-term conservation of Plant Genetic Resources (PGR) is a key priority for guaranteeing food security and sustainability of agricultural systems for current and future generations. The need for the secure conservation of genetic resources collections ex situ is critical, due to rapid and extreme climatic changes which are threatening and reducing biodiversity in their natural environments. The International Potato Center (CIP) conserves one of the most complete and diverse genetic resources collections of potato, with more than 7500 accessions composed of 4900 cultivated potato and 2600 potato wild relative accessions. The clonal conservation of cultivated potato, principally landraces, through in vitro or field collections is indispensable to maintain fixed allelic states, yet it is costly and labor-intensive. Cryopreservation, the conservation of biological samples in liquid nitrogen (-196°C), is considered the most reliable and cost-efficient long-term ex-situ conservation method for clonal crops. Over the last decade, CIP has built one of the largest potato cryobanks worldwide, cyopreserving more than 4000 cultivated potato accessions which represents 84% of the total cultivated potato collection currently conserved at CIP. In approximately, four years the entire potato collection will be cryopreserved. The development of an applied, robust cryopreservation protocol for potato, serves as a model for other clonally maintained crop collections. The CIP cryobank designs experiments with a high number of genetically diverse genotypes (70-100 accessions, seven cultivated species), to obtain reliable results that can be extrapolated over the collection as genotypes can often respond variably to the same applied conditions. Unlike most published reports on cryopreservation of plants, these large-scale experiments on potato are unique as they examine the acclimatization process of in vitro plants prior to, as well as during cryopreservation on up to ten times the number of genotypes conventionally reported in the published literature. As a result, an operational cryopreservation protocol for potato has advanced that works well across diverse potato accessions, not only with reduced processing time and costs, but also with an increased average full-plant recovery rate from 58% to 73% (+LN) for routine cryopreservation. The present article describes the composition of CIP's cryobank, the cryopreservation protocol, methodology for the dynamic improvement of the operational protocol, as well as data collected on regeneration from long term cryopreserved potatoes.

High level of somatic mutations detected in a diploid banana wild relative Musa basjoo.

Plants are thought to lack an early segregating germline and often retain both asexual and sexual reproduction, both of which may allow somatic mutations to enter the gametes or clonal progeny, and thereby impact plant evolution. It is yet unclear how often these somatic mutations occur during plant development and what proportion is transmitted to their sexual or cloned offspring. Asexual "seedless" propagation has contributed greatly to the breeding in many fruit crops, such as citrus, grapes and bananas. Whether plants in these lineages experience substantial somatic mutation accumulation is unknown. To estimate the somatic mutation accumulation and inheritance among a clonal population of plant, here we assess somatic mutation accumulation in Musa basjoo, a diploid banana wild relative, using 30 whole-genome resequenced samples collected from five structures, including leaves, sheaths, panicle, roots and underground rhizome connecting three clonal individuals. We observed 18.5 high proportion de novo somatic mutations on average between each two adjacent clonal suckers, equivalent to ~ 2.48 × 10-8 per site per asexual generation, higher than the per site per sexual generation rates (< 1 × 10-8) reported in Arabidopsis and peach. Interestingly, most of these inter-ramet somatic mutations were shared simultaneously in different tissues of the same individual with a high level of variant allele fractions, suggesting that these somatic mutations arise early in ramet development and that each individual may develop only from a few apical stem cells. These results thus suggest substantial mutation accumulation in a wild relative of banana. Our work reveals the significance of somatic mutation in Musa basjoo genetics variations and contribute to the trait improvement breeding of bananas and other asexual clonal crops.

Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas.

Hybridization and introgressions are important evolutionary forces in plants. They contribute to the domestication of many species, including understudied clonal crops. Here, we examine their role in the domestication of a clonal crop of outmost importance, banana (Musa ssp.). We used genome-wide SNPs generated for 154 diploid banana cultivars and 68 samples of the wild M. acuminata to estimate and geo-localize the contribution of the different subspecies of M. acuminata to cultivated banana. We further investigated the wild to domesticate transition in New Guinea, an important domestication center. We found high levels of admixture in many cultivars and confirmed the existence of unknown wild ancestors with unequal contributions to cultivated diploid. In New Guinea, cultivated accessions exhibited higher diversity than their direct wild ancestor, the latter recovering from a bottleneck. Introgressions, balancing selection and positive selection were identified as important mechanisms for banana domestication. Our results shed new lights on the radiation of M. acuminata subspecies and on how they shaped banana domestication. They point candidate regions of origin for two unknown ancestors and suggest another contributor in New Guinea. This work feed research on the evolution of clonal crops and has direct implications for conservation, collection, and breeding.

Signatures of selection in recently domesticated macadamia

Macadamia is a high value nut crop that is recently domesticated, ideal for testing the effect of artificial selection. Here, we sequence the genome of Hawaiian cultivar ‘Kau’ and assemble into 794 Mb in 14 pseudo-chromosomes with 37,728 genes. Genome analysis reveals a whole-genome duplication event, occurred 46.8 million years ago. Gene expansions occurred in gene families involves in fatty acid biosynthesis. Gene duplication of MADS-Box transcription factors in proanthocyanidin biosynthesis are relevant for seed coat development. Genome re-sequencing of 112 accessions reveals the origin of Hawaiian cultivars from Mount Bauple in southeast Queensland in Australia. Selective sweeps are detected in macadamia cultivars, including genes involved in fatty acid biosynthesis, seed coat development, and heat stress response. Such strong effects of artificial selection in few generations reveals the genomic basis for ‘one-step operation’ for clonal crop domestication. The knowledge gained could accelerate domestication of new crops from wild species.

Artificial selection optimizes clonality in chaya (Cnidoscolus aconitifolius)

The clonal propagation of crops offers several advantages to growers, such as skipping the juvenile phase, faster growth, and reduced mortality. However, it is not known if the wild ancestors of most clonal crops have a similar ability to reproduce clonally. Therefore, it is unclear whether clonality was an ancestral condition, or if it evolved during domestication in the majority of these crops. Here, I assessed some traits that are relevant to clonal propagation using stem cuttings from chaya (Cnidoscolus aconitifolius) and compared these traits to those of its wild ancestor. Chaya is highly relevant crop to food security in its domestication center (Yucatan Peninsula) and is now cultivated in several countries. Chaya is also an excellent model for assessing the effect of domestication on clonality because wild relatives and selection targets are known. Specifically, I compared resistance to desiccation, water and resource storage, as well as the production of new organs (shoots and leaves) by the stems of wild and domesticated plants. I also compared their performance in root development and clone survival. I found that, relative to their wild ancestors, the stem cuttings of domesticated chaya had 1.1 times greater storage capacity for water and starch. Additionally, the stems of domesticated plants produced 1.25 times more roots, 2.69 times more shoots and 1.94 more leaves, and their clones lived 1.87 times longer than their wild relatives. In conclusion, the results suggest that artificial selection has optimized water and starch storage by stems in chaya. Because these traits also confer greater fitness (i.e. increased fecundity and survival of clones), they can be considered adaptations to clonal propagation in the agroecosystems where this crop is cultivated.

Recovery of phenotypically normal transgenic potato plants is facilitated by regenerating multiple lines from transformation events: field validation using a cry9Aa2 gene conferring insect resistance

ABSTRACT A modified cry9Aa2 gene under the transcriptional control of the CaMV 35S promoter was transferred to four potato cultivars (‘Iwa’, ‘Karaka’, ‘Pacific’ and ‘Red Rascal’) using Agrobacterium-mediated gene transfer. Field plots were established for 170 independently regenerated transgenic lines derived from 113 transformation events. Phenotypic changes such as stunted plants, reduced vigour and/or leaf puckering, were observed in 29% of these lines. Foliage from the remaining 117 lines inhibited larval growth of potato tuber moth (Phthorimaea operculella Zeller) compared with non-transgenic controls. A high correlation was observed between greenhouse- and field-grown foliage for insect resistance using a detached leaf bioassay. Independently regenerated lines recovered from the same transformation event exhibited similar insect resistance. However, these lines derived from the same transformed cell differed markedly in phenotypic appearance and tuber yield. The first shoot regenerated from each transformation event was equivalent to the non-transgenic control for yield traits in only eight transformation events. A further 19 transformation events exhibited agronomic performance equivalent to the non-transgenic control when the second or subsequent regenerated shoots were evaluated. In clonal crops, multiple shoots from each transformation event should be independently assessed to ensure recovery of high-performing transgenic lines.

A simplified method for high recovery of kiwifruit (Actinidia spp.) shoot tips after droplet vitrification cryopreservation suitable for long-term conservation

Kiwifruit (Actinidia spp., Family Actinidiaceae) is a recently domesticated crop with highly endangered genetic resources in field genebanks and in the centre of diversity. Improved genotypes of several species in the genus have been commercialised and several other species are used in breeding programmes. Cryopreservation is considered a safe and cost-effective option for ex-situ conservation of clonal crops. In the current research we tested if the currently available method of droplet vitrification (DV) cryopreservation could be simplified whilst improving plant regeneration. Plant regeneration in the nine accessions belonging to A. chinensis var. chinensis, and A. chinensis var. deliciosa, A. arguta, A. macrosperma and A. polygama after cryopreservation ranged from 59 to 88% with the improved method where cold acclimation and antioxidant treatment steps were eliminated while sucrose pretreatment of shoot tips has been reduced to two steps in two days. Use of smaller (0.5–1 mm compared to 2 mm) in vitro shoot tips from younger (two weeks after subculture), fast-growing shoots and the use of liquid sucrose for shoot tip pretreatment are considered to be the reasons for this improved response. We also introduced the use of sodium dichloroisocyanurate as an alternative to household bleach as a sterilant for kiwifruit tissue culture establishment. The improved DV protocol is being used to cryopreserve valuable kiwifruit genetic resources with greater efficiency. Use of small shoot tips (0.5–1mm) from young shoots pretreated in liquid sucrose media in the dark significantly improved plant regeneration in five Actinidia species after droplet vitrification cryopreservation

Cryopreserving Clonal Crops: Increasing Processing Efficiency In Genebanks

Cryopreserving Clonal Crops: Increasing Processing Efficiency In Genebanks

Clonal crops show structural variation role in domestication.

The efficient use of clonal reproduction through vegetative propagation is one of the underlying reasons for the great success of the angiosperms, enabling stabilized and adapted phenotypes to rapidly expand into suitable environments1. This stability of phenotype has made clonal systems attractive for domestication, accounting for about half of all domesticated plants2. Despite the myth that clonal systems display little genetic variation having long been debunked3, they remain the poor relations in research, with relatively little known about how clonal systems adapt and evolve. Ironically, in this issue of Nature Plants, Zhou and colleagues4 show that it is precisely this quality of stable phenotype that make clonal systems suitable for demonstrating how genomic structural variation (SV) is a major driving force in the evolution of domesticates, and likely plants in general.

Two-stage selection in tea breeding

In breeding a clonal crop such as tea, selection is a two-stage process. In the first stage the highest yielding individual seedlings are chosen; these are then propagated and planted in clone trials in the second stage. A high selection intensity at the first stage risks eliminating most of the superior genotypes. The optimal proportion to be selected depends on the correlation between seedling ortet and clone performance. For yield this correlation is often fairly low, and in our trials with tea, selection of the highest yielding 15–25% of seedlings appears optimal. The ortet-clone correlation may be improved by more precise recording of ortet yields; in tea, this can be done by extending the recording period, to reduce the influence of year-to-year and seasonal variation. The relevance of these observations to other clonally propagated crops is discussed.

Propagation from Basal Epicormic Meristems Remediates an Aging-Related Disorder in Almond Clones

The asexual propagation of clonal crops has allowed cultivation of superior selections for thousands of years. With time, some clones deteriorate from genetic and epigenetic changes. Non-infectious bud-failure (NBF) in cultivated almond (Prunus dulcis) is a commercially important age-related disorder that results in the failure of new vegetative buds to grow in the spring, with dieback of terminal shoots, witches-brooming of surviving buds, and deformed bark (roughbark). The incidence of NBF increases with clone age, including within individual long-lived trees as well as nursery propagation lineages. It is not associated with any infectious disease agents. Consequently, nursery practices emphasize the establishment of foundation-mother blocks utilizing propagation-wood selected from proven and well-monitored propagation-lineages. Commercial propagation utilizes axillary shoot buds through traditional budding or grafting. This study examines NBF development using basal epicormic buds from individual trees of advanced age as an alternative source of foundation stock. Results show the age-related progression of NBF is suppressed in these epicormic meristems, possibly owing to their unique origins and ontogeny. NBF development in commercial orchards propagated from foundation blocks established from these sources was similarly dramatically suppressed even over the 10- to 20-year expected commercial orchard-life. Foundation-stock stability can be further maintained through appropriate management of propagation source-trees, which requires accurate knowledge of meristem origin and development.

Soil patterns and foliar standards for two cocoa clones in the States of Espírito Santo and Bahia, Brazil

ABSTRACT: The objective of this research was to establish soil patterns and foliar standards for clonal crops of cocoa CCN51 and PS1319 in the Atlantic regions within the northern Espírito Santo and southern Bahia States. Samples were collected from September to October 2015, in 45 high productive plots, being 23 plots of clone CCN51 and 22 of clone PS1319. Sufficiency ranges for soil and foliar standards were recommended for cocoa clones CCN51 and PS1319 planted in the Northern Espírito Santo and Southern Bahia states. Differences in the contents of foliar macronutrients K, Ca, Mg, S and micronutrients Fe and Mn, were verified between clones CCN51 and PS1319. Differences reported for standards from different geographical regions confirmed that these standards need to be regional and specific for different cocoa clones.

Cryobanking clonal crops: when knowledge and practice are not the same

Cryobanking clonal crops: when knowledge and practice are not the same

Genotype-aggregated planting improves yield in Jerusalem artichoke (Helianthus tuberosus) due to self/non-self-discrimination.

Accumulating evidence indicates that plants are capable of self/non‐self and kin/stranger discrimination. Plants increase biomass of and resource allocation to roots when they encounter roots of conspecific non‐self‐neighbors, but not when they encounter self roots. Root proliferation usually occurs at the expense of reproductive investment. Therefore, if clonal crops are capable of self/non‐self‐discrimination, spatially aggregated planting with seedlings of the same genotype may decrease root proliferation and produce a higher yield than planting without considering seedling genotype. To test this idea, we grew Helianthus tuberosus (Jerusalem artichoke) in pot and field conditions and examined self/non‐self‐discrimination and the effectiveness of genotype‐aggregated planting. Plants grown in self pairs allocated less to root biomass than plants grown in non‐self pairs in both pot and field conditions; in field conditions, the self pairs produced 40% more tubers by weight than the non‐self pairs. When six sprouts from seed tuber of two different genotypes were grown together, with the two genotypes planted aggregately (AGG) or alternately (ALT), plants in the AGG group produced 14% more tubers than plants in the ALT group. These results suggest that spatial aggregation of genotypes increases tuber production in H. tuberosus. Because we found no evidence for trade‐offs between root biomass and tuber production, suppression of root proliferation may not be the only mechanism behind the benefits of genotype aggregation. By applying the concept of self/non‐self‐discrimination, farmers can increase crop production without additional external inputs or expansion of agricultural land use.

Growing a population of cultivated cardoon (Cynara cardunculus var. altilis DC) for further selection as a reference energy crop

A population of cultivated cardoon (Cynara cardunculus var. altilis DC) was grown in Madrid (Spain) as a reference crop to select outstanding individuals for energy applications. The work was carried out within the frame of the Spanish funded projects PROBIOCOM (INIA) and FP13-ENER. Seeds for this work were produced by one of the partners of PROBIOCOM - the Agro-Energy Group of UPM - and came from a clonal crop (in vitro propagated plants) previously grown in Madrid. IMIDRA, as Head of that Project, established the reference crop according to the protocol for cardoon energy crop and was responsible for the crop. Seeds were sown in seed trays and once the plants had true leaves they were transplanted into the field. Collection of field data involved 449 individuals at the rosette stage and the dataset comprised the measurement of plant height, rosette diameter and leaf length; leaf type was determined as well. Individuals exhibiting larger leaf size were selected and categorized into two categories: undivided-like leaf blade (16 individuals) and pinnately lobed leaf blade (12 individuals). For these individuals, leaf fresh weight, number of leaves and leaf length of previously selected leaves were determined. Furthermore, three measurements were performed with a SPAD chlorophyll meter and the Munsell color chart. Morphological features were taken according CPVO-OCVV and UPOV protocols. Most plants exhibited pinnately leaves which generally resulted in larger sizes than the undivided-like leaf plants. Results suggested that the morphological plant type could be used as a preliminary selection criterion of C. cardunculus for biomass production; however, further studies are needed at harvest time to confirm this trend.