Induction and recovery of copy number variation in banana through gamma irradiation and low‐coverage whole‐genome sequencing

Traditional breeding methods are hindered in bananas due to the fact that major cultivars are sterile, parthenocarpic, triploid and thus clonally propagated. This has resulted in a narrow genetic base and limited resilience to biotic and abiotic stresses. Mutagenesis of in vitro propagated bananas is one method to introduce novel alleles and broaden genetic diversity. We previously established a method for the induction and recovery of single nucleotide mutations generated with the chemical mutagen EMS. However, officially released mutant banana varieties have been created using gamma rays, a mutagen that can produce large genomic insertions and deletions (indels). Such dosage mutations may be important for generating observable phenotypes in polyploids. In this study, we establish a low‐coverage whole‐genome sequencing approach in triploid bananas to recover large genomic indels caused by treatment with gamma irradiation. We first evaluated the commercially released mutant cultivar ‘Novaria’ and found that it harbours multiple predicted deletions, ranging from 0.3 to 3.8 million base pairs (Mbp). In total, predicted deletions span 189 coding regions. To evaluate the feasibility of generating and maintaining new mutations, we developed a pipeline for mutagenesis and screening for copy number variation in Cavendish bananas using the cultivar ‘Williams’. Putative mutations were recovered in 70% of lines treated with 20 Gy and 60% of the lines treated with 40 Gy. While deletion events predominate, insertions were identified in 20 Gy‐treated material. Based on these results, we believe this approach can be scaled up to support large breeding projects.     

Genetic dissimilarity of putative gamma-ray-induced 'Preciosa-AAAB-Pome type' banana (Musa sp) mutants based on multivariate statistical analysis

Bananas are among the most important fruit crops worldwide, being cultivated in more than 120 countries, mainly by small-scale producers. However, short-stature high-yielding bananas presenting good agronomic characteristics are hard to find. Consequently, wind continues to damage a great number of plantations each year, leading to lodging of plants and bunch loss. Development of new cultivars through conventional genetic breeding methods is hindered by female sterility and the low number of seeds. Mutation induction seems to have great potential for the development of new cultivars. We evaluated genetic dissimilarity among putative 'Preciosa' banana mutants generated by gamma-ray irradiation, using morphoagronomic characteristics and ISSR markers. The genetic distances between the putative 'Preciosa' mutants varied from 0.21 to 0.66, with a cophenetic correlation coefficient of 0.8064. We found good variability after irradiation of 'Preciosa' bananas; this procedure could be useful for banana breeding programs aimed at developing short-stature varieties with good agronomic characteristics.     

The Plantain Proteome,a Focus on Allele Specific Proteins Obtained from Plantain Fruits

Proteomics has been applied with great potential to elucidate molecular mechanisms in plants. This is especially valid in the case of non‐model crops of which their genome has not been sequenced yet, or is not well annotated. Plantains are a kind of cooking bananas that are economically very important in Africa, India, and Latin America. The aim of this work was to characterize the fruit proteome of common dessert bananas and plantains and to identify proteins that are only encoded by the plantain genome. We present the first plantain fruit proteome. All data are available via ProteomeXchange with identifier PXD005589. Using our in‐house workflow, we found 37 alleles to be unique for plantain covered by 59 peptides. Although we do not have access (yet) to whole‐genome sequencing data from triploid banana cultivars, we show that proteomics is an easily accessible complementary alternative to detect different allele specific SNPs/SAAPs. These unique alleles might contribute toward the differences in the metabolism between dessert bananas and plantains. This dataset will stimulate further analysis by the scientific community, boost plantain research, and facilitate plantain breeding.     

Molecular and cytological characterization of the global <Emphasis Type="Italic">Musa</Emphasis> germplasm collection provides insights into the treasure of banana diversity

Bananas (Musa spp.) are one of the main fruit crops grown worldwide. With the annual production reaching 144 million tons, their production represents an important contribution to the economies of many countries in Asia, Africa, Latin-America and Pacific Islands. Most importantly, bananas are a staple food for millions of people living in the tropics. Unfortunately, sustainable banana production is endangered by various diseases and pests, and the breeding for resistant cultivars relies on a far too small base of genetic variation. Greater diversity needs to be incorporated in breeding, especially of wild species. Such work requires a large and thoroughly characterized germplasm collection, which also is a safe depository of genetic diversity. The largest ex situ Musa germplasm collection is kept at the International Transit Centre (ITC) in Leuven (Belgium) and currently comprises over 1500 accessions. This report summarizes the results of systematic cytological and molecular characterization of the Musa ITC collection. By December 2015, 630 accessions have been genotyped. The SSR markers confirmed the previous morphological based classification for 84% of ITC accessions analyzed. The remaining 16% of the genotyped entries may need field verification by taxonomist to decide if the unexpected classification by SSR genotyping was correct. The ploidy level estimation complements the molecular data. The genotyping continues for the entire ITC collection, including newly introduced accessions, to assure that the genotype of each accession is known in the largest global Musa gene bank.     

Population dynamics of obligate cooperators

Obligate cooperative breeding species demonstrate a high rate of group extinction, which may be due to the existence of a critical number of helpers below which the group cannot subsist. Through a simple model, we study the population dynamics of obligate cooperative breeding species, taking into account the existence of a lower threshold below which the instantaneous growth rate becomes negative. The model successively incorporates (i) a distinction between species that need helpers for reproduction, survival or both, (ii) the existence of a migration rate accounting for dispersal, and (iii) stochastic mortality to simulate the effects of random catastrophic events. Our results suggest that the need for a minimum number of helpers increases the risk of extinction for obligate cooperative breeding species. The constraint imposed by this threshold is higher when helpers are needed for reproduction only or for both reproduction and survival. By driving them below this lower threshold, stochastic mortality of lower amplitude and/or lower frequency than for non-cooperative breeders may be sufficient to cause the extinction of obligate cooperative breeding groups. Migration may have a buffering effect only for groups where immigration is higher than emigration; otherwise (when immigrants from nearby groups are not available) it lowers the difference between actual group size and critical threshold, thereby constituting a higher constraint.     

Culture of Five Commonly Used Acid-Producing Bacteria on Banana Pulp

A significant fraction of the bananas and plantains produced in the humid tropics are wasted due to rapid spoilage. The use of acid-producing, anaerobic fermentation may be a safe and economical way to preserve the fruit in both large- and small-scale applications. The abilities of five commonly used, acid-producing bacteria to ferment media containing ripe or green bananas were examined. Three homofermentative bacteria, Lactobacillus bulgaricus, Streptococcus thermophilus, and Streptococcus faecalis, typically reduced the pH of a puree of ripe bananas from 4.8 to about 3.5 to 3.6 in 7 days at 37°C. Action on green bananas was similar, but the drop in pH was less pronounced. Very little gas evolved. Lactobacillus fermentum (formerly Lactobacillus fermenti) and Leuconostoc mesenteroides showed active gas evolution and a significant drop in pH. About twice as much gas evolved from ripe banana medium as from green bananas. The fermented purees were spongy, soft solids floating in a clear liquor. The color was medium to light creamy brown, and the odor was pleasant. Fermented products stored at room temperature retained good appearance and aroma throughout a 1-month storage test.     

Indica rice anther culture: can the impasse be surpassed?

During the past two decades numerous papers have been published on anther culture of rice. These studies clearly indicate that while anther culture is a technique that can be adopted for breeding japonica rice, it being a useful adjunct in indica rice breeding is still some way away. The main reasons why anther culture cannot be utilized for indica rice breeding is analyzed, and aspects that may be manipulated to achieve progress are presented in this review. The two stages of rice anther culture, callus induction and green plant regeneration, are genetically determined traits that show quantitative inheritance. Indica rice is known to have a recalcitrant genetic background that supports these traits poorly. While improvement of the genetic background through recombination or gene transfer remains possible, manipulation of culture media, particularly the nitrogen and carbon sources, has brought about substantial improvements in indica rice anther culture. Adjustments to pre- and post-culture conditions, that include application of various stresses on anthers before and after culture, also have had beneficial effects. The importance of reducing the tissue culture phase to achieve direct embryogenesis is discussed with special reference to improving green plant regeneration potential. The necessity to understand the processes involved in microspore embryogenesis is highlighted in order to support empirical knowledge and achieve a breakthrough in technology. In this regard, rice genome sequence information may be leveraged to elucidate functions of genes involved in microspore embryogenesis.     

Carbon footprint of a Cavendish banana supply chain

Purpose

Bananas are one of the highest selling fruits worldwide, and for several countries, bananas are an important export commodity. However, very little is known about banana’s contribution to global warming. The aims of this work were to study the greenhouse gas emissions of bananas from cradle to retail and cradle to grave and to assess the potential of reducing greenhouse gas (GHG) emissions along the value chain.

Methods

Carbon footprint methodology based on ISO-DIS 14067 was used to assess GHG emissions from 1 kg of bananas produced at two plantations in Costa Rica including transport by cargo ship to Norway. Several methodological issues are not clearly addressed in ISO 14067 or the LCA standards 14040 and ISO 14044 underpinning 14067. Examples are allocation, allocation in recycling, representativity and system borders. Methodological choices in this study have been made based on other standards, such as the GHG Protocol Products Standard.

Results and discussion

The results indicate that bananas had a carbon footprint (CF) on the same level as other tropical fruits and that the contribution from the primary production stage was low. However, the methodology used in this study and the other comparative studies was not necessarily identical; hence, no definitive conclusions can be drawn. Overseas transport and primary production were the main contributors to the total GHG emissions. Including the consumer stage resulted in a 34 % rise in CF, mainly due to high wastage. The main potential reductions of GHG emissions were identified at the primary production, within the overseas transport stage and at the consumer.

Conclusions

The carbon footprint of bananas from cradle to retail was 1.37 kg CO₂ per kilogram banana. GHG emissions from transport and primary production could be significantly reduced, which could theoretically give a reduction of as much as 44 % of the total cradle-to-retail CF. The methodology was important for the end result. The choice of system boundaries gives very different results depending on which life cycle stages and which unit processes are included. Allocation issues were also important, both in recycling and in other processes such as transport and storage. The main uncertainties of the CF result are connected to N₂O emissions from agriculture, methane emissions from landfills, use of secondary data and variability in the primary production data. Thus, there is a need for an internationally agreed calculation method for bananas and other food products if CFs are to be used for comparative purposes.     

Ecology and community dynamics of Kubo people in the tropical lowlands of Papua New Guinea

Kubo producer-units (families and independent bachelors) could have been self-sufficient in the production of bananas but chose not to be. Nor did they seek self-sufficiency in the production of any combination of staple carbohydrate foods (bananas, tubers, sago flour) or, in the long term, strive for balance in the exchange of food with other producer-units. Despite the fact that bananas, which provided 50% of people's energy needs, were a delayed-return crop Kubo communities were very unstable. This instability and the failure to choose the option of self-sufficiency were connected and were mediated through intense intracommunity sharing that, ultimately, served to negotiate a concern with sorcery. The people grew bananas in the way they did, not out of environmental necessity, but to accommodate the crop to the needs of sharing and, thereby, facilitate community living.     

Quarantine security of bananas at harvest maturity against Mediterranean and Oriental fruit flies (Diptera: Tephritidae) in Hawaii

Culled bananas (dwarf 'Brazilian', 'Grand Nain', 'Valery', and 'Williams') sampled from packing houses on the islands of Hawaii, Kauai, Maui, Molokai, and Oahu identified specific "faults" that were at risk from oriental fruit fly, Bactrocera dorsalis (Hendel), infestation. Faults at risk included bunches with precociously ripened bananas, or bananas with tip rot, fused fingers, or damage that compromised skin integrity to permit fruit fly oviposition into fruit flesh. No Mediterranean fruit fly, Ceratitis capitata (Wiedemann), or melon fly, B. cucurbitae (Coquillett), infestations were found in culled banana samples. Field infestation tests indicated that mature green bananas were not susceptible to fruit fly infestation for up to 1 wk past the scheduled harvest date when attached to the plant or within 24 h after harvest. Recommendations for exporting mature green bananas from Hawaii without risk of fruit fly infestation are provided. The research reported herein resulted in a USDA-APHIS protocol for exporting mature green bananas from Hawaii.     

Defining core habitat of local populations of the gray treefrog (Hyla versicolor) based on choice of oviposition site

Concern over amphibian population declines and loss of terrestrial and aquatic habitat have emphasized the need to define habitat requirements for each stage in a species' life history. The realization that pond-breeding amphibians spend most of their lives in the terrestrial environment suggests the need to protect terrestrial as well as aquatic habitat. Many studies on amphibian populations have focused on emigration from breeding sites to define habitat use; however these studies do not typically elucidate terrestrial activities of adults within the breeding season. We measured colonization rates of artificial pools by gray treefrogs (Hyla versicolor) at multiple distances from natural breeding ponds. We found a non-random distribution of egg deposition among distances, with 95% of eggs deposited within 15 m of the breeding pond. Additionally, we found that the time to first colonization of artificial pools increased with respect to distance. Our results indicate that adult gray treefrogs may travel up to 200 m within a breeding season, and that multiple breeding ponds may be considered part of a single population. We suggest that a minimum core terrestrial habitat of 60 m surrounding breeding sites is appropriate for protection of local populations of gray treefrogs.     

对虾转基因研究的现状和展望

随着生物技术的发展,通过基因工程手段获得对虾新品种成为可能,然而经过十几年努力,目前对虾转基因研究依然处于初级阶段。各国科学家正在加紧研究,争取有所突破。综述了近年来国内外对虾转基因研究的进展以及目前面临的技术和安全问题,同时对未来对虾的转基因技术发展和应用前景进行了讨论 。     

Microbiological and physicochemical factors affecting <Emphasis Type="Italic">Aspergillus</Emphasis> section <Emphasis Type="Italic">Flavi</Emphasis> incidence in Cavendish banana (<Emphasis Type="Italic">Musa cavendishii</Emphasis>) chips production in Southern Philippines

Microbiological and physicochemical factors affecting the incidence of Aspergillus section Flavi in dried Cavendish banana (Musa cavendishii) chips production in Southern Philippines were examined. The average counts of Aspergillus section Flavi (AFC) in fresh and dried Cavendish bananas from 10 production batches of the Philippine Agro-Industrial Development Cooperative in Davao del Norte, Southern Philippines were 1.2 × 10² and 1.6 × 10² cfu/g, respectively. Isolates from both samples were identified to be Aspergillus flavus based on spore type and conidial structure of isolates. An increasing trend in the AFC of Cavendish bananas was observed during dried banana chips processing. Variability in the AFC between production batches was attributed to differences in aerobic and fungal populations and physicochemical characteristics of the fruits, peel damage of the raw materials, concentration of AFC in the air and food-contact surfaces of the production area, and temperature and relative humidity (RH) conditions of the environment during production and storage. Physicochemical characteristics of Cavendish bananas from the receipt of raw materials up to the first day of drying were within the reported range of values allowing growth and toxin production by aflatoxigenic fungi. Air-borne AFC varied depending on the section of the production area examined. The close proximity of the waste disposal area from the production operation to the preparation, drying and storage areas suggests that cross-contamination, probably air-borne or insect-borne was a likely occurrence. The hands of workers were also identified as AFC sources. Results of this study highlight the need for the development of strategies to control aflatoxigenic fungi and aflatoxin contamination in Philippine dried Cavendish bananas.     

Repetitive part of the banana (<Emphasis Type="Italic">Musa acuminata</Emphasis>) genome investigated by low-depth 454 sequencing

Background  

Bananas and plantains (Musa spp.) are grown in more than a hundred tropical and subtropical countries and provide staple food for hundreds of millions of people. They are seed-sterile crops propagated clonally and this makes them vulnerable to a rapid spread of devastating diseases and at the same time hampers breeding improved cultivars. Although the socio-economic importance of bananas and plantains cannot be overestimated, they remain outside the focus of major research programs. This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement.     

Effects of pair migratory behavior on breeding phenology and success in a partially migratory shorebird population

In migratory systems, variation in individual phenology can arise through differences in individual migratory behaviors, and this may be particularly apparent in partial migrant systems, where migrant and resident individuals are present within the same population. Links between breeding phenology and migratory behavior or success are generally investigated at the individual level. However, for breeding phenology in particular, the migratory behaviors of each member of the pair may need to be considered simultaneously, as breeding phenology will likely be constrained by timing of the pair member that arrives last, and carryover effects on breeding success may vary depending on whether pair members share the same migratory behavior or not. We used tracking of marked individuals and monitoring of breeding success from a partially migrant population of Eurasian oystercatchers (Haematopus ostralegus) breeding in Iceland to test whether (a) breeding phenology varied with pair migratory behavior; (b) within‐pair consistency in timing of laying differed among pair migratory behaviors; and (c) reproductive performance varied with pair migratory behavior, timing of laying, and year. We found that annual variation in timing of laying differed among pair migratory behaviors, with resident pairs being more consistent than migrant and mixed pairs, and migrant/mixed pairs breeding earlier than residents in most years but later in one (unusually cold) year. Pairs that laid early were more likely to replace their clutch after nest loss, had higher productivity and higher fledging success, independent of pair migratory behavior. Our study suggests that the links between individual migratory behavior and reproductive success can vary over time and, to a much lesser extent, with mate migratory behavior and can be mediated by differences in laying dates. Understanding these cascading effects of pair phenology on breeding success is likely to be key to predicting the impact of changing environmental conditions on migratory species.     

Effects of latitude on the trade-off between reproduction and moult: a long-term study with pied flycatcher

Long-distance migratory passerine birds are generally time constrained by reproduction and moult, which need to be completed before migration. Breeding and post-nuptial moult may overlap especially under time-constrained conditions (northern latitudes). Here, we analysed the timing of adult moult in relation to latitude, timing of breeding and reproductive effort in pied flycatchers (Ficedula hypoleuca) breeding in four widely separated populations (40-68° N). In males but not females, the proportion of moulting birds while provisioning nestlings increased with increasing latitude. This may suggest that a moult-breeding overlap is a strategy employed by male pied flycatchers to adjust to the short breeding season at northern latitudes. However, the moult-breeding overlap was more pronounced among males in the southernmost study population (Spain). In this population, males may decide not to invest more in reproduction, and start moulting at earlier breeding stage than in northern populations,or, alternatively, birds in the Mediterranean region are time constrained by the hot and dry summer. The trade-off between breeding and post-nuptial moult may be more important in some populations than in others, depending on the latitude of the breeding site. Our results show that a moult-breeding overlap imposes a fitness cost on males in terms of fecundity and breeding success.     

Effect of medium osmotic potential on callus induction and shoot regeneration in flax anther culture

Development of an efficient and cost-effective doubled haploid production system in flax (Linum usitatissimum L.) is the prerequisite for the application of doubled haploid technology in a practical breeding program. Pre-culture of anthers on a medium containing 15% sucrose for 2–7 days before transfer to the same medium containing 6% sucrose for a total of 28 days culture period significantly increased shoot regeneration for all four genotypes evaluated. Moreover, pre-culture of anthers on medium containing 15% sucrose for 2–7 days was sufficient to dramatically reduce the frequency of shoot regeneration from somatic tissues and thereby to increase the frequency of microspore-derived plants in flax anther culture. Furthermore, replacing 15% sucrose with 6% sucrose and 9% polyethylene glycol (PEG), or 3% sucrose and 12% PEG, in pre-culture medium did not significantly affect callus induction and shoot regeneration. The results indicate that sucrose may act as carbon/energy source as well as an osmotic regulator in flax anther culture. Sucrose as an osmotic regulator may be replaced by a non-metabolizable osmoticum: PEG. The implication of this study in flax anther culture and breeding is discussed.     

Mutation induction and tissue culture in improving fruits

This review describes in vitro mutation induction methods in fruits and the in vitro selection procedures available for early screening. Results obtained through in vitro mutation techniques, including somaclonal variation, are reviewed and compared with the current achievements and future prospects of transgenic breeding. Plant improvement based on mutations, which change one or a few specific traits of a cultivar, can contribute to fruit improvement without altering the requirements of fruit industry. Induced mutations have well defined limitations in fruit breeding applications, but their possibilities may be expanded by the use of in vitro techniques. Tissue culture increases the efficiency of mutagenic treatments for variation induction, handling of large populations, use of ready selection methods, and rapid cloning of selected variants. Molecular techniques can provide a better understanding of the potential and limitations of mutation breeding e.g. molecular marker-assisted selection, which can lead to the early identification of useful variants. The relatively high number of research reports compared with the low number of cultivars released suggests that mutagenesis in combination with tissue culture is either ineffective or has yet to be exploited in fruits. Positive achievement recorded in other species seem to support the hypothesis that in vitro mutation induction has high potential also for fruit improvement. The possible contribution of a well-pondered and coordinated use of the numerous mutation induction, mutant selection, and field validation procedures available to advances in fruit breeding is discussed. This revised version was published online in June 2006 with corrections to the Cover Date.     

氰戊菊酯在香蕉及蕉园土壤中的残留动态与安全性评价

采用气相色谱(GC-ECD)及田间试验方法,研究氰戊菊酯在香蕉及蕉园土壤中的残留降解动态。结果表明,氰戊菊酯在香蕉上的原始残留沉积量因不同施药处理有所差异,香蕉及蕉园土壤上的降解速度较缓慢,降解规律符合“C＝C₀·^e-kt”一级动力学关系。在香蕉上,相关系数r = 0.9722～0.9980(P＜0.01),降解系数k = 0.0703～0.0767,半衰期T_1/2 = 9.1～9.9 d,降解99%所需要时间T_0.99 = 60.1～65.6 d;在土壤中,k = 0.0821,T_1/2 = 8.5 d,T_0.99 = 56.1 d。距第2次施药后62～68 d,最终香蕉的残留量＜0.01 mg·kg^-1,土壤中为0.015～0.020 mg·kg^-1。在福建蕉区,氰戊菊酯的常规施药方法是间隔期7 d连续2次施用有效剂量112.50 g·hm^-2,采样前安全间隔期可推荐为＞13.6 d,产品质量最终可符合GB/T 2763-2012、NY/T 750-2011的要求。