Development of rice (Oryza sativa) lines resistant to aryloxyphenoxypropionate herbicides through induced mutation with gamma rays

The aryloxyphenoxypropionate herbicides (APPs) are graminicides with excellent control of many grass weeds species, including weedy rice (Oryza sativa L.). These herbicides block the fatty acid biosynthesis by inhibiting the enzyme acetyl‐CoA carboxylase (ACCase), resulting in the death of susceptible plants. Inducing mutation with gamma rays to rice seeds, two lines resistant to APPs herbicides were developed. Plant dose–response assays confirmed the resistance to the APPS herbicides quizalofop‐p‐ethyl and haloxyfop‐p‐methyl. The carboxyltransferase domain fragments of ACCase from the resistant biotype and susceptible control were sequenced and compared. A point mutation was detected in the amino acid position 2,027 (Rice Genome Annotation Project: Os05g22940.1). Results indicated that resistance to APPs is a consequence of an altered ACCase enzyme that confers resistance. The use of APPs herbicide‐resistant rice lines represents an innovative and promising alternative for weedy rice control in paddy rice systems.     

Allelic polymorphism and inheritance of MdACS1 and MdACO1 genes in apple (Malus × domestica Borkh.)

The allelic polymorphism and inheritance of MdACS1 and MdACO1 genes were analysed in 28 apple cultivars, which were derived from reciprocal crosses of the following parental pairs: ‘Golden Delicious’ × ‘James Grieve’, ‘Golden Delicious’ × ‘Jonathan’, ‘Cox's Orange Pippin’ × ‘Golden Delicious’, ‘Cox's Orange Pippin’ × ‘Jonathan’. Polymorphisms were detected by PCR and the use of two restriction enzymes (BamH1 and RsaI). In addition, new primers were designed for the further discrimination of MdACO1 alleles. Two alleles of MdACS1 gene (MdACS1‐1 and MdACS1‐2) and three alleles of MdACO1 gene (a, b and c) were detected. Cloning and sequencing of MdACO1 alleles confirmed a high conservation and some differences within the coding regions and helped to reconcile between different numbering systems. Observed segregations confirmed that alleles a, b and c belonged to the MdACO1 gene. It is apparent that polymorphisms within the MdACS1 and MdACO1 genes could aid cultivar genotyping and identification and, furthermore, that the MdACS1‐2/2 genotype is correlated with a long apple storage life.     

SFB‐based S‐haplotyping of apricot (Prunus armeniaca) with DHPLC

Most cultivars that belong to the Rosaceae are self‐incompatible and depend on cross‐pollination. The pollen donor and pollen recipient have to flower synchronously and must be genetically compatible. Genetic compatibility is governed by the S‐locus, which holds the S‐RNase and S‐haplotype‐specific F‐Box (SFB) genes. Thus, the S‐genotype of cultivars is an important feature and is characterized molecularly by the S‐RNase and SFB alleles which are distinctive for each S‐haplotype. Here, we report the usage of DNA chromatography (denaturing high‐performance liquid chromatography – DHPLC) for identifying the S‐genotypes of European apricots on the basis of their SFB alleles. DHPLC is amenable to high‐throughput automation, and therefore is valuable for breeding and for high‐quality plant typing in the nursery.     

Genomic selection allowing for marker‐by‐environment interaction

Genomic selection has been routinely implemented in plant breeding in two stages. The first stage usually omits the marker information and estimates adjusted means of genotypes across environments. The second stage uses the adjusted means to predict genomic breeding values. However, if the effects of markers vary substantially between different environments, it may be important to account for this variation for varieties adapted to different environments. Using two maize data sets, we investigated whether modelling the marker‐by‐environment interaction can improve the predictive ability of genomic selection relative to modelling genotype‐by‐environment interaction alone. Modelling the marker‐by‐environment interaction did not substantially increase the predictive ability relative to modelling only the genotype‐by‐environment interaction for the two tested data sets. Thus, genomic selection, carried out in a stagewise fashion, such that the marker information is omitted until the last stage of the process, may suffice for most practical purposes. Moreover, predictive ability did not reduce substantially even when the number of markers with consistent effects across environments used for genomic prediction was reduced to about 50.     

Structured regionalism in the Asia‐Pacific: Slow but sure progress

Abstract: Notwithstanding the existence of considerable intra‐regional trade, the Asia‐Pacific region was slow to catch onto the concept and phenomenon of regionalism. Not many regional integration arrangements were created in the region and the ones that were created did not go far. Over the preceding three‐and‐a‐half decades, the high performing Asian economies adopted outward‐oriented strategies, promoting brisk trade expansion trade and foreign investment. Asia‐Pacific regionalism was essentially market‐led and uninstitutionalised. Regional production networks were the consequence of market‐led economic dynamics in the region. Large corporations, including transnationals, contributed to the growth of a pan‐Asian industrialisation process and trade expansion. This scenario underwent a transformation in the 1990s, particularly during the Asian crisis of 1997–98. Conscious economic and monetary co‐operation with institutional support increased considerably. Asia‐Pacific economies are more committed to regionalism – both economically and institutionally – now than ever before.     

Identification and characterization of new S‐alleles associated with self‐incompatibility in almond

Almond is a highly heterozygous species with a high number of S‐alleles controlling its gametophytic self‐incompatibility system (GSI). In this work, we have analysed 14 Spanish local almond cultivars for S‐RNase allele diversity. Five new S‐RNase alleles were identified by cloning and sequencing, S₃₁ (804 bp) in ‘Pou de Felanitx’ and ‘Totsol’, S₃₂ (855 bp) in ‘Taiatona’, S₃₃ (1165 bp) in ‘Pou d’Establiments’ and ‘Muel’, S₃₄ (1663 bp) in ‘Pané‐Barquets’ and S₃₅ (1658 bp) in ‘Planeta de les Garrigues’. Additionally, seven already known almond alleles could be recognized in the local cultivars studied. The high number of new alleles identified reveals the wide diversity of almond germplasm still existing and requiring characterization, and points to the possibility of new findings by a wider study focusing on other provenances. The almond S‐RNases have been compared to those of other Prunus species, showing a high identity and confirming that the S‐RNase gene in this genus presents a probable common ancestor.     

Introduction to special issue: Meeting the challenges of HIV/AIDS in Southeast and East Asia

Out of a total of 38 million people living with HIV/AIDS globally today, the Asia‐Pacific is home to about 7.4 million – a figure which constitutes a sharp rise to previous years. In absolute numbers, infections in Asia are projected to exceed African figures within a decade. This has largely to do with economic changes towards market‐based capitalism, widening socioeconomic disparities and increased levels of mobility (internal and cross‐border), as for instance in China and Indonesia. Overall, the epidemic in Asia has been described as more complex than in Africa involving a multiplicity of transmission modes. The case studies presented in the contributions to this special issue discuss the connections between issues of mobility, gender, (trans)nationalism and sexuality in understanding the HIV/AIDS challenge in the region. The various ways in meeting the challenges of HIV/AIDS in Southeast and East Asia are analysed, whereby non‐governmental and community‐based responses often emerge as more effective than state interventions.     

Trial heterogeneity and variance models in the genetic evaluation of potato tuber yield

Genetic evaluation aims to identify genotypes with high empirical breeding values (EBVs) for selection as parents. In this study, 2157 potato genotypes were evaluated for tuber yield using 8 years of early‐stage trial data collected from a potato breeding programme. Using linear mixed models, spatial parameters to target greater control of localised spatial heterogeneity within trials were estimated and variance models to account for across‐trial genetic heterogeneity were tested. When spatial components improved model fit, correlations of errors were mostly small and negative for marketable tuber yield (MTY) and total tuber yield (TTY), suggesting the presence of interplot competition in some years. For the analysis of multi‐environment trials, a variance model with a simple correlation structure (with heterogeneous variances) was the most favourable variance structure fitted for TTY and PTY (per cent marketable yield). There was very little difference in model fit when comparing a factor analytic structure of order 2 (FA2) with either FA1 or simple correlation structures for MTY, indicating that simple variance models may be preferable for early‐stage genetic evaluation of potato yield.     

A high‐resolution einkorn (Triticum monococcum L.) linkage map involving wild,domesticated and feral einkorn genotypes

A high‐resolution consensus linkage map of Triticum monococcum was assembled from two separate maps involving domesticated, feral and wild einkorn wheat accessions. The genotyping‐by‐sequencing (GBS) approach based on DArTseq markers yielded overstretched maps. Deleting all markers with missing data and then converting dubious singletons to missing data produced two maps of about 1,380 cM, close to the published genome size. The consensus map spanned 1,562 cM, had one bin mapped every 0.92 cM and showed only one gap > 10 cM. Chromosome length varied between 151 cM (chromosome 4) and 270 cM (chromosome 7). The consensus map was compared to other A‐genome maps, and the sequences of genetically mapped DArTseq were used to anchor contigs of the T. monococcum, T. urartu and T. aestivum draft genomes based on sequence homology to assess colinearity and to assign mapped markers to the seven chromosomes of the bread wheat A‐genome. Finally, an in silico functional characterization of the sequences was performed. This high‐resolution map will facilitate QTL and association analysis and assist the genome assembly of the einkorn genome.     

Cloning,characterization and overexpression of a 14‐3‐3 ω protein from oil palm (Elaeis guineensis)

Plant 14‐3‐3 proteins are involved in signal transduction pathways of nitrogen and carbohydrate metabolism. An Eg14‐3‐3 ω gene was isolated from the mesocarp of oil palm. The 1055‐bp cDNA had an open reading frame of 774 bp that encoded for 258 amino acids, and the cDNA had 113‐bp and 195‐bp 5′‐ and 3′‐untranslated regions, respectively. The calculated molecular weight was 28.06 kDa, with a pI of 5.04. The palm 14‐3‐3 showed closest identity to 14‐3‐3 proteins of the omega group. The entire sequence of Eg14‐3‐3 ω showed 83% identity with 14‐3‐3 protein isoform 16R from Solanum tuberosum. Phylogenetic analysis showed that the Eg14‐3‐3 isoform was within the omega (ω) subgroup and, thus, was designated Eg14‐3‐3 ω. The Eg14‐3‐3 ω expression patterns were strong in the mesocarp as compared to the root. When Eg14‐3‐3 ω cDNA was overexpressed in transgenic calli, there was higher accumulation of oil in the transgenic calli than in the controls. Therefore, Eg14‐3‐3 ω has potential for applications in the breeding of oil palms in the future.     

The development of specific SNP markers for chromosome 14 in cotton using next‐generation sequencing

Lacking of reference genome sequence for the development of stable molecular markers for specific chromosomes (intervals) remains to be a challenge in cotton, which was a necessary step in fine mapping of gene (QTL). In this study, the feasibility of development of single‐nucleotide polymorphism (SNP) markers between CS‐B14Sh (a substitution line for short arm of Chromosome 14) and TM‐1 (the recurrent parent) was explored using next‐generation sequencing (NGS) based on reduced representation libraries (RRLs). High‐quality genome sequences, representing about 7.1%, 8.8% and 10.4% of the tetraploid cotton genome, were generated for TM‐1, 3‐79 (the donor parent) and CS‐B14Sh, respectively. A total of 397 putative SNP markers were detected between CS‐B14Sh and TM‐1, and most (358) of them were also detected between TM‐1 and 3‐79. Allele‐specific PCR method was used for validation of 40 SNP markers, and 27 of them showed polymorphism between TM‐1 and CS‐B14Sh, and a linkage group comprising of 25 SNP markers and five SSR markers was constructed. The order of SNP markers agreed well with the position of them on Chr05 of D genome, which further approved the truth of SNPs detected. The results suggested that the development of SNP markers in specific genome region using NGS was efficient in substitution or near‐isogenic lines.     

Photosynthesis is Reduced,and Seeds Fail to Set and Fill at Similar Soil Water Contents in Grass Pea (Lathyrus sativus L.) Subjected to Terminal Drought

Grass pea (Lathyrus sativus L.) is an indeterminate grain legume considered adapted to dry environments, but the mechanisms of its adaptation are not well understood. Grass pea plants were exposed to terminal drought from podding, and the development of water deficit was measured together with its effects on leaf photosynthesis, stomatal conductance, carbon remobilisation to the seeds, flower production and abortion, pod production and abortion, seed set, seed growth and the neurotoxin β‐N‐oxalyl‐L‐a, β‐diaminopropionic acid (β‐ODAP) concentration. Predawn leaf water potential (Ψ_leaf), stomatal conductance (gs), rate of leaf photosynthesis (Pn), flower production, pod production, filled pod number, seed number, seed size and yield decreased, while flower abortion, pod abortion and seed abortion increased, and the concentration of β‐ODAP was unchanged under terminal drought conditions. gs and Pn began to decrease at a higher plant‐available soil water content (PAWC) (67.2 ± 2.3 % and 62.9 ± 2.3 %) than Ψ_leaf (43.7 ± 1.1 %). Flowers and pods ceased being produced only when the PAWC decreased below 40.1 ± 4.6 % and 35.3 ± 3.0 %, respectively, but seed set and seed growth ceased when PAWC decreased below 55.5 ± 1.6 % and 58.0 ± 3.7 %, respectively. The mobilization of ¹³C labelled assimilates from the stems was greater under terminal drought than under well‐watered conditions, but the transfer to the seed was small. We conclude that seed set and seed growth decreased as the soil dried due to a reduction in current photosynthesis as a result of stomatal closure.