The Significance of Wild Plants in the Evolutionary Ecology of Three Major Viruses Infecting Cultivated Sweetpotato in Uganda

The studies presented in this thesis contribute to the understanding of evolutionary ecology of three major viruses threatening cultivated sweetpotato (Ipomoea batatas Lam) in East Africa: Sweet potato feathery mottle virus (SPFMV; genus Potyvirus; Potyviridae), Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus; Closteroviridae) and Sweet potato mild mottle virus (SPMMV; genus Ipomovirus; Potyviridae). The viruses were serologically detected and the positive results confirmed by RT-PCR and sequencing. SPFMV was detected in 24 wild plant species of family Convolvulacea (genera Ipomoea, Lepistemon and Hewittia), of which 19 species were new natural hosts for SPFMV. SPMMV and SPCSV were detected in wild plants belonging to 21 and 12 species (genera Ipomoea, Lepistemon and Hewittia), respectively, all of which were previously unknown to be natural hosts of these viruses. SPFMV was the most abundant virus being detected in 17% of the plants, while SPMMV and SPCSV were detected in 9.8% and 5.4% of the assessed plants, respectively. Wild plants in Uganda were infected with the East African (EA), common (C), and the ordinary (O) strains, or co-infected with the EA and the C strain of SPFMV. The viruses and virus-like diseases were more frequent in the eastern agro-ecological zone than the western and central zones, which contrasted with known incidences of these viruses in sweetpotato crops, except for northern zone where incidences were lowest in wild plants as in sweetpotato. The NIb/CP junction in SPMMV was determined experimentally which facilitated CP-based phylogenetic and evolutionary analyses of SPMMV. Isolates of all the three viruses from wild plants were genetically similar to those found in cultivated sweetpotatoes in East Africa. There was no evidence of host-driven population genetic structures suggesting frequent transmission of these viruses between their wild and cultivated hosts. The p22 RNA silencing suppressor-encoding sequence was absent in a few SPCSV isolates, but regardless of this, SPCSV isolates incited sweet potato virus disease (SPVD) in sweetpotato plants co-infected with SPFMV, indicating that p22 is redundant for synergism between SCSV and SPFMV. Molecular evolutionary analysis revealed that isolates of strain EA of SPFMV that is largely restricted geographically in East Africa experience frequent recombination in comparison to isolates of strain C that is globally distributed. Moreover, non-homologous recombination events between strains EA and C were rare, despite frequent co-infections of these strains in wild plants, suggesting purifying selection against non-homologous recombinants between these strains or that such recombinants are mostly not infectious. Recombination was detected also in the 5 - and 3 -proximal regions of the SPMMV genome providing the first evidence of recombination in genus Ipomovirus, but no recombination events were detected in the characterized genomic regions of SPCSV. Strong purifying selection was implicated on evolution of majority of amino acids of the proteins encoded by the analyzed genomic regions of SPFMV, SPMMV and SPCSV. However, positive selection was predicted on 17 amino acids distributed over the whole the coat protein (CP) in the globally distributed strain C, as compared to only 4 amino acids in the multifunctional CP N-terminus (CP-NT) of strain EA largely restricted geographically to East Africa. A few amino acid sites in the N-terminus of SPMMV P1, the p7 protein and RNA silencing suppressor proteins p22 and RNase3 of SPCSV were also submitted to positive selection. Positively selected amino acids may constitute ligand-binding domains that determine interactions with plant host and/or insect vector factors. The P1 proteinase of SPMMV (genus Ipomovirus) seems to respond to needs of adaptation, which was not observed with the helper component proteinase (HC-Pro) of SPMMV, although the HC-Pro is responsible for many important molecular interactions in genus Potyvirus. Because the centre of origin of cultivated sweetpotato is in the Americas from where the crop was dispersed to other continents in recent history (except for the Australasia and South Pacific region), it would be expected that identical viruses and their strains occur worldwide, presuming virus dispersal with the host. Apparently, this seems not to be the case with SPMMV, the strain EA of SPFMV and the strain EA of SPCSV that are largely geographically confined in East Africa where they are predominant and occur both in natural and agro-ecosystems. The geographical distribution of plant viruses is constrained more by virus-vector relations than by virus-host interactions, which in accordance of the wide range of natural host species and the geographical confinement to East Africa suggest that these viruses existed in East African wild plants before the introduction of sweetpotato. Subsequently, these studies provide compelling evidence that East Africa constitutes a cradle of SPFMV strain EA, SPCSV strain EA, and SPMMV. Therefore, sweet potato virus disease (SPVD) in East Africa may be one of the examples of damaging virus diseases resulting from exchange of viruses between introduced crops and indigenous wild plant species. Keywords: Convolvulaceae, East Africa, epidemiology, evolution, genetic variability, Ipomoea, recombination, SPCSV, SPFMV, SPMMV, selection pressure, sweetpotato, wild plant species Author s Address: Arthur K. Tugume, Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O Box 27, FIN-00014, Helsinki, Finland. Email: tugume.arthur@helsinki.fi Author s Present Address: Arthur K. Tugume, Department of Botany, Faculty of Science, Makerere University, P.O. Box 7062, Kampala, Uganda. Email: aktugume@botany.mak.ac.ug, tugumeka@yahoo.com

Streptomyces scabies and S. turgidiscabies as pathogens causing potato common scab, and potential methods for their control

Tieteellinen tiivistelmä Common scab is one of the most important soil-borne diseases of potato (Solanum tuberosum L.) in many potato production areas. It is caused by a number of Streptomyces species, in Finland the causal agents are Streptomyces scabies (Thaxter) Lambert & Loria and S. turgidiscabies Takeuchi. The scab-causing Streptomyces spp. are well-adapted, successful plant pathogens that survive in soil also as saprophytes. Control of these pathogens has proved to be difficult. Most of the methods used to manage potato common scab are aimed at controlling S. scabies, the most common of the scab-causing pathogens. The studies in this thesis investigated S. scabies and S. turgidiscabies as causal organisms of common scab and explored new approaches for control of common scab that would be effective against both species. S. scabies and S. turgidiscabies are known to co-occur in the same fields and in the same tuber lesions in Finland. The present study showed that both these pathogens cause similar symptoms on potato tubers, and the types of symptoms varied depending on cultivar rather than the pathogen species. Pathogenic strains of S. turgidiscabies were antagonistic to S. scabies in vitro indicating that these two species may be competing for the same ecological niche. In addition, strains of S. turgidiscabies were highly virulent in potato and they tolerated lower pH than those of S. scabies. Taken together these results suggest that S. turgidiscabies has become a major problem in potato production in Finland. The bacterial phytotoxins, thaxtomins, are produced by the scab-causing Streptomyces spp. and are essential for the induction of scab symptoms. In this study, thaxtomins were produced in vitro and four thaxtomin compounds isolated and characterized. All four thaxtomins induced similar symptoms of reduced root and shoot growth, root swelling or necrosis on micro-propagated potato seedlings. The main phytotoxin, thaxtomin A, was used as a selective agent in a bioassay in vitro to screen F1 potato progeny from a single cross. Tolerance to thaxtomin A in vitro and scab resistance in the field were correlated indicating that the in vitro bioassay could be used in the early stages of a resistance breeding program to discard scab-susceptible genotypes and elevate the overall levels of common scab resistance in potato breeding populations. The potential for biological control of S. scabies and S. turgidiscabies using a non-pathogenic Streptomyces strain (346) isolated from a scab lesion and S. griseoviridis strain (K61) from a commercially available biocontrol product was studied. Both strains showed antagonistic activity against S. scabies and S. turgidiscabies in vitro and suppressed the development of common scab disease caused by S. turgidiscabies in the glasshouse. Furthermore, strain 346 reduced the incidence of S. turgidiscabies in scab lesions on potato tubers in the field. These results demonstrated for the first time the potential for biological control of S. turgidiscabies in the glasshouse and under field conditions and may be applied to enhance control of common scab in the future.

Perunan Y-viruksen testaaminen korkeassa happi-hiilidioksidipitoisuudessa idätetyistä perunoista

Perunalla (Solanum tuberosum L.) tällä hetkellä maailmanlaajuisesti eniten sato- ja laatutappioita aiheuttaa perunan Y-virus (PVY). Vaikka pelkän Y-viruksen aiheuttamaa satotappiota on vaikea mitata, on sen arvioitu olevan 20-80 %. Viruksen tärkein leviämistapa on viroottinen siemenperuna. Korkealaatuinen siemenperuna on edellytys ruoka-, ruokateollisuus- ja tärkkelysperunan tuotannolle. Kasvuston silmämääräinen tarkastelu aliarvioi yleensä Y-viruksen esiintyvyyttä. Laboratoriotestauksen avulla saadaan tarkempi tieto pellolta korjatun sadon saastunta-asteesta. Ongelmana Y-viruksen testaamisessa on, että sitä ei havaita dormanssissa olevista perunoista otetuista näytteistä yhtä luotettavasti kuin jo dormanssin ohittaneista perunoista testattaessa. Erilaisia menetelmiä kemikaaleista (Rindite, bromietaani) kasvihormoneihin (mm. gibberelliinihappo) ja varastointiolosuhteiden muutoksiin (kylmä- ja lämpökäsittely) on kokeiltu perunan dormanssin purkamiseen, mutta tulokset ovat olleet vaihtelevia. Tässä tutkielmassa perunan dormanssin purkamiseen käytettiin happi-hiilidioksidikäsittelyä (O2 40 % ja CO2 20 %) eripituisina käsittelyaikoina. Tarkoituksena oli selvittää, vaikuttaako käsittely perunan itämiseen ja dormanssin luontaista aikaisempaan purkautumiseen tai Y-viruksen havaitsemiseen. Lisäksi haluttiin selvittää, voiko Y-viruksen määrittämisen ELISA-testillä (Enzyme Linked Immunosorbent Assay) tehdä yhtä luotettavasti myös muista kasvinosista (mukula, itu), kuin tällä hetkellä yleisesti käytetystä perunan lehdestä. Idätyskäsittelyn vaikutuksista dormanssin purkautumiseen saatiin vaihtelevia, eikä kovinkaan yleistettäviä tuloksia. Käsittelyn ei myöskään havaittu vaikuttavan PYY-viroottisuuden havaitsemiseen eri näytemateriaaleilla testattaessa. Kun eri kasvinosien toimivuutta testissä vertailtiin, mukulamateriaalin todettiin aliarvioivan PVY-viroottisuutta kaikissa kokeissa. Myös itumateriaali aliarvioi pääsääntöisesti PVY-viroottisuutta ELISA:lla tehdyissä määrityksissä. Luotettavin testimateriaali oli perunan lehti.

Timotein (Phleum pratense ssp. pratense L.) alkuperän vaikutus kylmänkestävyyteen, vernalisaatiovaatimukseen sekä kasvuun ja kehitykseen

Nurmiheinien merkitys maailmanlaajuisesti on merkittävä, sillä noin 69 % maapallon peltopinta-alasta on pysyvää laidunmaata tai niittyä. Suomessa nurmien osuus on noin 29 %, ja tuotanto perustuu pääosin intensiiviseen säilörehuntuotantoon. Yleisin nurmiheinälaji Suomessa on timotei (Phleum pratense ssp. pratense L.). Timotei on talvenkestävä ja soveltuu siksi pohjoisiin kasvuoloihin. Timoteilajikkeita jalostettaessa pohjoista alkuperää olevia vanhempaislinjoja käytetään hyvän talvenkestävyyden varmistamiseksi, eteläisiä tavoiteltaessa nopeaa kasvurytmiä. Ilmaston muutoksen ennustetaan lisäävän erilaisia äärioloja kuten myrskyjä ja sateita. Vuorokauden keskilämpötila nousee ja kasvukausi pidentyy. Lisäksi talvet muuttuvat sateisemmiksi. Muutokset näkyvät erityisesti pohjoisissa kasvuympäristöissä. Tutkimuksessa haluttiinkin selvittää eri alkuperää edustavien timoteilajikkeiden ja linjojen kylmänkestävyyttä, kasvu-, ja kehitysnopeutta sekä vernalisaation vaikutusta. Lisäksi tutkittiin syysviljojen vernalisaatiovasteen mittaamiseen käytettyjen menetelmien soveltuvuutta nurmille. Tutkimukseen kuului kaksivuotinen peltokoe sekä kasvatuskaappikoe. Vernalisaatio nopeutti timotein kasvua ja kehitystä. Tutkimuksen perusteella eteläistä alkuperää olevilla lajikkeilla kasvu- ja kukintavalmius oli olemassa ilman vernalisaatiota. Pohjoisilla lajikkeilla oli suurempi vernalisaatiovaste ja niiden kukkiminen ja kasvu nopeutui vernalisaation myötä. Vernalisaatiolla oli vaikutusta myös kasvuston rakenteeseen. Generatiivisten versojen määrä lisääntyi vernalisaation myötä, kun taas vegetatiivisten versojen määrä väheni. Kylmänkestävyys oli tutkimuksen perusteella riippuvainen syksyn karaistumisjakson pituudesta sekä jakson lämpösummasta (FH-COLD). Korkea keskilämpötila ja lyhyt karaistumisjakso heikensivät kylmänkestävyyttä. Vastaavasti karaistumiskauden lämpötilan ollessa välillä 0 °C:ta ja + 5 °C:ta ja jakson pituuden kasvaessa kylmänkestävyys lisääntyi. Tutkimuksen perusteella vernalisaatiolla oli selvä vaikutus timotein kasvuun ja kehitykseen. Pohjoista alkuperää olevat timoteit reagoivat vernalisaatioon eteläisiä enemmän. Osa pohjoisista linjoista vaati vernalisaation generatiivisten versojen muodostumiseen. Syysviljojen vernalisaatiovasteen mittausmenetelmät soveltuvat osin myös puhtaiden timoteilajikkeiden vernalisaation seurantaan.

青蒿异源基因的遗传转化及青蒿生物合成相关基因的克隆

本论文由三部分内容组成，一、药用青蒿的遗传转化，即根癌农杆菌和发 根农杆菌介导的转化系统的建立及其影响参数的研究。二、青蒿素生物合成的 分子调控。三、倍半萜生物合成相关基因的克隆。 一、药用青蒿的遗传转化。建立了Ri质粒介导和Ti质粒介导的两种转基因系统， 其中Ri质粒介导青蒿转基因系统的建立是国际上首次报道;以GFP基因为报 告基因，首次获得高效表达的青蒿转绿色荧光蛋白基因的丛生芽，并对GFP基 因的表达进行了组织和细胞水平的定位。此外，对影响两种转基因系统的主要 参数进行了较为详细的研究。上述研究为青蒿素生物合成的分子调控奠定了坚 实的基础。 二、青蒿素生物合成的分子调控。为探索提高青蒿植株或组织和器官中的青蒿 素含量，首次以棉花中克隆的杜松烯合成酶和法呢基焦磷酸合成酶的 cDNA 为 目的基因导入青蒿，对青蒿中青蒿素的生物合成进行了分子调控研究的尝试。 通过已建立的两种转基因系统，将从棉花中克隆的杜松烯合成酶和法呢基焦磷 酸合成酶的 cDNA 导入青蒿，获得转基因发根和转基因植株。结果表明，外源 基因的表达能够影响青蒿素的生物合成，其中法呢基焦磷酸合成酶基因的过量 表达能够促进青蒿素的生物合成，提高转基因发根和植株中的青蒿素的含量。 转基因发根F-26系中青蒿素含量最高达3.01 mg/g.DW，与对照相比青蒿素含量 提高3～4倍;转基因植株的青蒿素含量最高达10.08 mg/g.DW，与对照相比， 转基因植株的青蒿素产物提高2～3倍。此外，研究还表明，在转基因的发根C -37株系中，外源杜松烯合成酶基因的导入和表达可能相应地促进青蒿转基因 发根自身的法昵基焦磷酸基因的表达。 三、倍半萜生物合成相关基因的克隆。采用 RT-PCR 技术，从马铃薯 (Solanum tuberosum L.) 幼叶中克隆了 HMGRII 亚基因家族的一个新的成员 HMGR-c2（GenBank accession No．AF 096838Southem）;杂交分析表明，该基因至少以 两个拷贝以上形式存在于马铃薯基因组中;RT-PCR分析表明，HMGR -c2的 表达在幼苗期无组织特异性，广泛地存在于根、茎、叶等组织中。以青蒿001 株系的苗期叶片为材料，构建了青蒿苗期的λgtll cDNA文库，以PCR筛库方 法从青蒿中克隆一个法呢基焦磷酸合成酶cDNA (Artfps2 GenBank accession No． AF136602)和一个HMGR cDNA(GenBank accession No．AF142473);以青蒿 025株系的苗期叶片为材料，构建了青蒿苗期部分质粒文库以 PCR 筛库方法从 青蒿中克隆一个法昵基焦磷酸合成酶 cDNA (Artfpsl GenBank accession No.AF112881);此外，还从青蒿中克隆了倍半萜合成酶的 cDNA 片段(GenBank accession No.AF156854)。其中青蒿倍半萜合成酶基因的克隆是目前国际上本研 究领域最受关注的焦点和难点之一。至此，本研究已将与青蒿素生物合成相关 的三个重要的关键酶基因基本克隆，这无疑将加速青蒿素生物合成的基础和应 用研究的进程。

不同保水剂对宁南山区马铃薯生长发育和产量的影响

为促进宁南半干旱山区产业支柱作物马铃薯的生产,解决马铃薯生产、特别是苗期的干旱缺水问题,采用田间试验方法,进行PAM保水剂、多功能保水剂与一定配方尿素+过磷酸钙的施用对马铃薯生长发育、产量及效益的试验。结果表明,两种保水剂均能促进马铃薯生长发育,增加干物质积累,但是在不同生育时期促进作物生长的效果有所不同。1%PAM保水剂浸种2~3 min处理在前期效果显著,多功能保水剂在后期效果突出。马铃薯以施用多功能保水剂30 kg/hm2效果最好,其产量和商品薯分别比对照高出52.33%、138.29%,增收5 356.8元/hm2。研究表明,施用30 kg/hm2多功能保水剂比用1%PAM保水剂浸种2~3min更适宜宁南半干旱区及其同类地区旱地种植马铃薯。

不同类型作物对干湿交替环境的反应

通过对干湿交替环境下春小麦、马铃薯、大豆和玉米等作物的产量、水分利用效率及光合作用、蒸腾作用、气孔导度等生理变化的研究表明 :( 1 )春小麦和马铃薯在干湿交替环境下可获得与充分供水相当的产量而它们的水分利用效率却显著提高 ,大豆减产幅度较大 ,玉米减产严重 ,其水分利用效率显著低于全湿处理 ;( 2 )浇水后各作物的光合速率、蒸腾速率和气孔导度都有所增加 ,但不同作物增加的幅度不同 ,就是同一作物各指标的增幅也不同 ;( 3)干湿交替环境下同化物的运输模式有利于春小麦籽粒的充实和马铃薯块茎的膨大 ,而不利于玉米产量的形成 ;( 4 )产量不仅决定于营养生长阶段 ,更主要决定于生殖生长阶段。此外 ,还就干湿交替过程中若干生理变化和经济产量形成机制作了初步探讨。

Profiling phytochemical and nutritional components of potato

Potatoes (Solanum Tuberosum L.) contain secondary metabolites that may have an impact on human health. The aim of this study was to assess the levels of some of these compounds in a wide range of varieties, including rare, heritage and commercial cultivars. Vitamin C, total carotenoids, phenolics, flavonoids, antioxidant activity and glycoalkaloids were determined, using spectroscopy and chromatography, in the skin and flesh of tubers grown in field trials. Transcript levels of key synthetic enzymes were assessed by qPCR. Accumulation of selected metabolites was higher in the skin than in the flesh of tubers, except ascorbate, which was undetected in the skin. Differences were on average 2.5 to 3-fold for carotenoids, 6-fold for phenolics, 15 to 16-fold for flavonoids, 21-fold for glycoalkaloids and 9 to 10-fold for antioxidant activity. Higher contents of carotenoids were associated with yellow skin or flesh, and higher values of phenolics, flavonoids and antioxidant activity with blue flesh. Variety ‘Burren’ had maxima values of carotenoids in skin and flesh, variety ‘Nicola’ of ascorbate, variety ‘Congo’ of phenolics, flavonoids and antioxidant activity in both tissues, except antioxidant activity in the skin, which was higher in ‘Edzell Blue’. Varieties ‘May Queen’ and ‘International Kidney’ had highest glycoalkaloid content in skin and flesh respectively. The effect of the environment was diverse: year of cultivation was significant for all metabolites, but site of cultivation was not for carotenoids and glycoalkaloids. Levels of expression of phenylalanine ammonia-lyase and chalcone synthase were higher in varieties accumulating high contents of phenolic compounds. However, levels of expression of phytoene synthase and L-galactono-1,4-lactone dehydrogenase were not different between varieties showing contrasting levels of carotenoids and ascorbate respectively. This work will help identify varieties that could be marketed as healthier and the most suitable varieties for extraction of high-value metabolites such as glycoalkaloids.

Curvas de tuberización : IV influencia de algunos factores en la pérdida de peso de papa almacenada

p.145-158

Papas Chips XI : materia seca, peso específico, rendimiento y fijación de aceite, parámetros de calidad

p.145-150

Survey of Agricultural Practices and Alternatives to Pesticide Use to Conserve Water Resources in the Mojanda Watershed, Ecuador

Agriculture in the Mojanda Watershed is facing rainfall reductions caused by climate change. Reductions of water availability in the Watershed are also due to constant extension of the agricultural activities into the páramo ecosystem above 3000m a.s.l., with this ecosystem having immanently important functions in the local water balance. The application of pesticides threatens the quality of water and with less precipitation contaminations will further concentrate in the outflow. To analyze problems associated with agricultural practices in the area a questionnaire about agricultural practices (28) was conducted and fields (20) were surveyed for pests and diseases with a focus on potatoes (Solanum tuberosum L.), tree tomatoes (Solanum betaceum Cav.) and peas (Pisum sativum L.). Potatoes were infected to a low degree with Phytophthora infestans and according to the farmers the Andean potato weevil (Premnotrypes spec.) caused biggest losses. To combat the weevil the soils are disinfected with toxic Carbofuran (WHO Class 1B). Tree tomatoes showed symptoms of various fungal diseases. Most important was Fusarium solani causing the branches to rot and Anthracnosis (Colletotrichum gloeosporioides) causing the fruits to rot. Fungicide applications were correspondingly high. Peas were only minorly affected by Ascochyta blight (Mycosphaerella pinodes) and a root rot. Overall 19 active ingredients were applied of which fungicide Mancozeb (WHO class table 5) and insecticide Carbofuran (WHO Class 1B) were applied the most. Approved IPM methods are advised to reduce pesticide use. For tree tomatoes regular cutting of branches infected with F. solani and regular collection and disposal of infected fruits with Anthracnosis are advised. For potatoes plastic barriers around the fields prevent the Andean potato weevil from laying eggs thus reducing infestation with the larvae in the tubers. Local bioinsecticide “Biol” seems effective and without harm to the environment, although not used by many farmers. Organic fertilization promises to restore decreasing soil fertility, water holding capacity and reduce erosion. The here presented alternatives and strategies to reduce pesticide use pose an opportunity to preserve the water resources of the region.

Farmers’ knowledge and perceptions of potato pests and their management in Uganda

As we initiate entomological research on potato (Solanum tuberosum L.) in Uganda, there is need to understand farmers’ knowledge of existing insect pest problems and their management practices. Such information is important for designing a suitable intervention and successful integrated pest management (IPM) strategy. A farm household survey using a structured questionnaire was conducted among 204 potato farmers in six districts of Uganda (i.e., Kabale, Kisoro, Mbale, Kapchorwa, Mubende, and Kyegegwa) during August and September 2013. Diseases, insect pests, price fluctuations, and low market prices were the four highest ranked constraints in potato production, in order of decreasing importance. Cutworms (Agrotis spp.), aphids (Myzus persicae (Sulzer)), and potato tuber moth (Phthorimaea operculella (Zeller)) were the three most severe insect pests. Ants (Dorylis orantalis Westwood), whiteflies (Bemisia tabaci (Gennadius)), and leafminer flies (Liriomyza huidobrensis (Blanchard)) were pests of moderate importance. Major yield losses are predominantly due to late blight (Phytophthora infestans (Mont.) de Bary) and reached 100% without chemical control in the districts of Kabale, Kisoro, Mbale, and Kapchorwa. On average, farmers had little to moderate knowledge about pest characteristics. The predominant control methods were use of fungicides (72% of respondents) and insecticides (62% of respondents). On average, only 5% of the 204 farmers knew about insect pests and their natural enemies. This lack of knowledge calls for training of both farmers and extension workers in insect pest identification, their biology, and control. Empowering farmers with knowledge about insect pests is essential for the reduction of pesticide misuse and uptake of more environmentally friendly approaches like IPM. Field surveys would need follow-up in order to assess the actual field infestation rates and intensities of each insect pest and compare the results with the responses received from farmers.

Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.)

The deployment of genetic markers is of interest in crop assessment and breeding programmes, due to the potential savings in cost and time afforded. As part of the internationally recognised framework for the awarding of Plant Breeders’ Rights (PBR), new barley variety submissions are evaluated using a suite of morphological traits to ensure they are distinct, uniform and stable (DUS) in comparison to all previous submissions. Increasing knowledge of the genetic control of many of these traits provides the opportunity to assess the potential of deploying diagnostic/perfect genetic markers in place of phenotypic assessment. Here, we identify a suite of 25 genetic markers assaying for 14 DUS traits, and implement them using a single genotyping platform (KASPar). Using a panel of 169 UK barley varieties, we show that phenotypic state at three of these traits can be perfectly predicted by genotype. Predictive values for an additional nine traits ranged from 81 to 99 %. Finally, by comparison of varietal discrimination based on phenotype and genotype resulted in correlation of 0.72, indicating that deployment of molecular markers for varietal discrimination could be feasible in the near future. Due to the flexibility of the genotyping platform used, the genetic markers described here can be used in any number or combination, in-house or by outsourcing, allowing flexible deployment by users. These markers are likely to find application where tracking of specific alleles is required in breeding programmes, or for potential use within national assessment programmes for the awarding of PBRs.

Bio-fortification of potato tubers using foliar zinc-fertiliser

Worldwide, many people are zinc (Zn)-deficient. Dietary Zn intake can be increased by producing crops with higher concentrations of Zn in their edible portions. This can be achieved by applying Zn-fertilisers to varieties with an increased ability to acquire Zn and to accumulate Zn in their edible portions. Potato (Solanum tuberosum L.) is an important food crop and is, therefore, a target for bio-fortification with Zn. Field trials incorporating a core collection of 23 potato genotypes, performed over 4 years (2006 – 2009), indicated significant genotypic effects on tuber Zn concentration and suggested that tuber Zn concentration was influenced by environmental effects, but also found that genotype environment (G E) interactions were not significant. Tuber Zn concentrations averaged 10.8 mg kg–1 dry matter (DM), and the ratio between the lowest and the highest varietal tuber Zn-concentration averaged 1.76. Tuber Zn concentrations could be increased by foliar Zn-fertilisation. Tuber yields of ‘Maris Piper’ were unaffected by foliar applications of < 1.08 g Zn plant–1. The relationship between tuber Zn concentration and foliar Zn application followed a saturation curve, reaching a maximum at approx. 30 mg Zn kg–1 DM at a foliar Zn application rate of 1.08 g plant–1. Despite a 40-fold increase in shoot Zn concentration compared to the unfertilised controls following foliar Zn fertilisation with 2.16 g Zn plant–1, only a doubling in tuber Zn concentration was observed. This suggests that the biofortification of tubers with Zn was restricted by the limited mobility of Zn in the phloem. A significant positive linear relationship between tuber Zn concentration and tuber N concentration supported the hypothesis of co-transport of Zn and N-compounds in the phloem.

Molecular and phenotypic characterization of the alternative seasonal growth habit and flowering time in barley (Hordeum vulgare ssp. vulgare L.)

Barley can be classified into three major agronomic types, based on its seasonal growth habit (SGH): spring, winter and alternative. Winter varieties require exposure to vernalization to promote subsequent flowering and are autumn-sown. Spring varieties proceed to flowering in the absence of vernalization and are sown in the spring. The ‘alternative’ (also known as ‘facultative’) SGH is only loosely defined and can be sown in autumn or spring. Here, we investigate the molecular genetic basis of alternative barley. Analysis of the major barley vernalization (VRN-H1, VRN-H2) and photoperiod (PPD-H1, PPD-H2) response genes in a collection of 386 varieties found alternative SGH to be characterized by specific allelic combinations. Spring varieties possessed spring loci at one or both of the vernalization response loci, combined with long-day non-responsive ppd-H1 alleles and wild-type alleles at the short-day photoperiod response locus, PPD-H2. Winter varieties possessed winter alleles at both vernalization loci, in combination with the mutant ppd-H2 allele conferring delayed flowering under short-day photoperiods. In contrast, all alternative varieties investigated possessed a single spring allele (either at VRN-H1 or at VRN-H2) combined with mutant ppd-H2 alleles. This allelic combination is found only in alternative types and is diagnostic for alternative SGH in the collection studied. Analysis of flowering time under controlled environment found alternative varieties flowered later than spring control lines, with the difference most pronounced under short-day photoperiods. This work provides genetic characterization of the alternative SGH phenotype, allowing precise manipulation of SGH and flowering time within breeding programmes, and provides the molecular tools for classification of all three SGH categories within national variety registration processes.