Whole‐genome profiling and shotgun sequencing delivers an anchored,gene‐decorated,physical map assembly of bread wheat chromosome 6A

Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence‐based physical map of wheat chromosome 6A using whole‐genome profiling (WGP^?). The bacterial artificial chromosome (BAC) contig assembly tools fingerprinted contig (fpc ) and linear topological contig (ltc ) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that ltc created a highly robust assembly compared with those formed by fpc . The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the long arm, with an L₅₀ of 1 Mb. To facilitate in silico anchoring, WGP^? tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to the ‘decoration’ of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the sequencing of wheat chromosome 6A, and is of immediate use for map‐based isolation of agronomically important genes/quantitative trait loci located on this chromosome.     

Hive‐stored pollen of honey bees: many lines of evidence are consistent with pollen preservation,not nutrient conversion

Honey bee hives are filled with stored pollen, honey, plant resins and wax, all antimicrobial to differing degrees. Stored pollen is the nutritionally rich currency used for colony growth and consists of 40–50% simple sugars. Many studies speculate that prior to consumption by bees, stored pollen undergoes long‐term nutrient conversion, becoming more nutritious ‘bee bread’ as microbes predigest the pollen. We quantified both structural and functional aspects associated with this hypothesis using behavioural assays, bacterial plate counts, microscopy and 454 amplicon sequencing of the 16S rRNA gene from both newly collected and hive‐stored pollen. We found that bees preferentially consume fresh pollen stored for <3 days. Newly collected pollen contained few bacteria, values which decreased significantly as pollen were stored >96 h. The estimated microbe to pollen grain surface area ratio was 1:1 000 000 indicating a negligible effect of microbial metabolism on hive‐stored pollen. Consistent with these findings, hive‐stored pollen grains did not appear compromised according to microscopy. Based on year round 454 amplicon sequencing, bacterial communities of newly collected and hive‐stored pollen did not differ, indicating the lack of an emergent microbial community co‐evolved to digest stored pollen. In accord with previous culturing and 16S cloning, acid resistant and osmotolerant bacteria like Lactobacillus kunkeei were found in greatest abundance in stored pollen, consistent with the harsh character of this microenvironment. We conclude that stored pollen is not evolved for microbially mediated nutrient conversion, but is a preservative environment due primarily to added honey, nectar, bee secretions and properties of pollen itself.     

陕南鄂西丘陵麦区小麦HMW-GS组成和LMW-GS等位基因变异

采用SDS-PAGE凝胶电泳和STS标记方法分别对陕南鄂西丘陵麦区小麦品种(系)中的高分子量谷蛋白亚基(HMW-GS)组成和低分子量谷蛋白亚基(LMW-GS)Glu-A3与Glu-B3位点的等位基因进行了检测,并通过STS特异性标记对SDS-PAGE凝胶电泳检测的HMW-GS部分结果进行了验证。结果表明:(1)陕南麦区64份小麦材料中共检测到9种HMW-GS类型,其中Glu-A1位点含有Null、1共2种等位变异,频率分别为53.12%和46.88%;Glu-B1位点有7+8、7+9、14+15和17+18共4个等位变异,频率分别为26.56%、48.44%、21.88%和3.13%;Glu-D1位点有2+12、5+10和4+12共3种等位变异,频率为71.88%、15.63%和12.49%;而且17种不同亚基组合中以"1,7+9,2+12"与"Null,7+9,2+12"为主。(2)64份小麦材料中检测到11种LMW-GS类型,其中Glu-A3位点存在Glu-A3a、Glu-A3c和Glu-A3d共3种等位变异,分布频率为10.94%、62.50%和26.56%;GluB3位点有Glu-B3a、Glu-B3b、Glu-B3d、Glu-B3e、Glu-B3f、Glu-B3g、Glu-B3i和Glu-B3j共8种等位变异,分布频率分别为6.25%、4.69%、29.69%、1.56%、3.13%、18.75%、4.69%、31.25%。(3)2个特异性STS标记对SDSPAGE凝胶电泳检测到的HMW-GS部分组成结果验证表明,STS标记可以有效克服SDS-PAGE方法检测小麦HMW-GS中的7与7*、8与8*以及2与2*亚基的误读问题,为小麦品质育种与食品加工提供理论支持。     

Spelt and emmer flours: characterization of the lactic acid bacteria microbiota and selection of mixed starters for bread making

Aims: This study aimed at characterizing the lactic acid bacteria microbiota and selecting mixed endogenous starters to be used for sourdough fermentation of spelt or emmer flours. Methods and Results: Identification of lactic acid bacteria was carried out by partial sequencing of the 16S rRNA, recA, 16S/23S rRNA spacer region and pheS genes. Spelt flour showed the largest biodiversity, while Lactobacillus plantarum dominated in emmer flour. Isolates were subjected to RAPD‐PCR analysis and screened based on the kinetics of growth and acidification, quotient of fermentation and liberation of free amino acids (FAA) during sourdough fermentation. After selection, mixed starters were used according to a two‐step fermentation process. Wheat flour was fermented by the same starters. Spelt and emmer sourdoughs had slightly higher pH than wheat sourdoughs but titratable acidity, concentration of FAA and phytase activity were higher. Specific volume and crumb grain of emmer and, especially, spelt breads approached those of wheat breads. Sensory analysis confirmed the suitability of spelt and emmer for bread making. Conclusions: The sourdough biotechnology was indispensable to completely exploit the potential of spelt and emmer flours. Significance and Impact of the Study: Results filled up the lack of knowledge on the lactic acid bacteria microbiota and technological performances of spelt and emmer flours.     

Occurrence and function of yeasts in Asian indigenous fermented foods

In the Asian region, indigenous fermented foods are important in daily life. In many of these foods, yeasts are predominant and functional during the fermentation. The diversity of foods in which yeasts predominate ranges from leavened bread-like products such as nan and idli, to alcoholic beverages such as rice and palm wines, and condiments such as papads and soy sauce. Although several products are obtained by natural fermentation, the use of traditional starter cultures is widespread. This minireview focuses on the diversity and functionality of yeasts in these products, and on opportunities for research and development.     

黄淮麦区小麦品种(系)中Yr26基因的SSR检测

选用与Yr26紧密连锁的SSR标记Xgwm11和Xgwm18结合田间抗性鉴定,对239份黄淮麦区小麦品种(系)进行检测,以明确Yr26基因在黄淮麦区小麦品种资源中的分布.结果表明:共有35份品种(系)含有与Yr26紧密连锁的SSR标记Xgwm18或Xgwm11的特征带,占检测样本的14.6%.在这35份材料中,31份田间抗性鉴定表现免疫至中抗,4份表现中感.分子标记检测与田间抗病性检测吻合度较好,该标记可以用于Yr26基因的分子标记辅助选择.综合分子标记和田间鉴定,31份小麦(系)含有Yr26基因,占102份抗病材料的30.39%.     

A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function

Aegilops tauschii (Coss.) Schmal. (2n=2x=14, DD) (syn. A. squarrosa L.; Triticum tauschii) is well known as the D-genome donor of bread wheat (T. aestivum, 2n=6x=42, AABBDD). Because of conserved synteny, a high-density map of the A. tauschii genome will be useful for breeding and genetics within the tribe Triticeae which besides bread wheat also includes barley and rye. We have placed 249 new loci onto a high-density integrated cytological and genetic map of A. tauschii for a total of 732 loci making it one of the most extensive maps produced to date for the Triticeae species. Of the mapped loci, 160 are defense-related genes. The retrotransposon marker system recently developed for cultivated barley (Hordeum vulgare L.) was successfully applied to A. tauschii with the placement of 80 retrotransposon loci onto the map. A total of 50 microsatellite and ISSR loci were also added. Most of the retrotransposon loci, resistance (R), and defense-response (DR) genes are organized into clusters: retrotransposon clusters in the pericentromeric regions, R and DR gene clusters in distal/telomeric regions. Markers are non-randomly distributed with low density in the pericentromeric regions and marker clusters in the distal regions. A significant correlation between the physical density of markers (number of markers mapped to the chromosome segment/physical length of the same segment in m) and recombination rate (genetic length of a chromosome segment/physical length of the same segment in m) was demonstrated. Discrete regions of negative or positive interference (an excess or deficiency of crossovers in adjacent intervals relative to the expected rates on the assumption of no interference) was observed in most of the chromosomes. Surprisingly, pericentromeric regions showed negative interference. Islands with negative, positive and/or no interference were present in interstitial and distal regions. Most of the positive interference was restricted to the long arms. The model of chromosome structure and function in cereals with large genomes that emerges from these studies is discussed.     

Dynamic viscoelasticity of protease-treated rice batters for gluten-free rice bread making

Papain (cysteine protease), subtilisin (Protin SD-AY10, serine protease), and bacillolysin (Protin SD-NY10, metallo protease) increased the specific volume of gluten-free rice breads by 19–63% compared to untreated bread. In contrast, Newlase F (aspartyl protease) did not expand the volume of the rice bread. In a rheological analysis, the viscoelastic properties of the gluten-free rice batters also depended on the protease categories. Principal component analysis (PCA) analysis suggested that the storage and loss moduli (G′ and G″, respectively) at 35 °C, and the maximum values of G′ and G″, were important factors in the volume expansion. Judging from the PCA of the viscoelastic parameters of the rice batters, papain and Protin SD-AY10 improved the viscoelasticity for gluten-free rice bread making, and Protin SD-NY effectively expanded the gluten-free rice bread. The rheological properties differed between Protin SD-NY and the other protease treatments.     

TaCOLD1 defines a new regulator of plant height in bread wheat

Plant height is among the most important agronomic traits that influence crop yield. However, in addition to the Rht‐1 alleles, the molecular basis of plant height in bread wheat remains largely unclear. Based on wheat gene expression profiling analysis, we identify a light‐regulated gene from bread wheat, designated as TaCOLD1, whose encoding protein is homologous to cold sensor COLD1 in rice. We show that TaCOLD1 protein is localized to the endoplasmic reticulum (ER) and plasma membrane. Phenotypic analyses show that overexpression of a mutated form of TaCOLD1 (M187K) in bread wheat cultivar Kenong199 (Rht‐B1b) background resulted in an obvious reduction in plant height. Further, we demonstrate that the hydrophilic loop of TaCOLD1 (residues 178–296) can interact with TaGα‐7A (the α subunit of heterotrimeric G protein) protein but not TaGα‐1B, and the mutation (M187K) in TaCOLD1 remarkably enhances its interaction with TaGα‐7A. Physical interaction analyses show that the C‐terminal region of TaGα‐7A, which is lacking in the TaGα‐1B protein, is necessary for its interaction with TaCOLD1. Intriguingly, the C‐terminal region of TaGα‐7A is also physically associated with the TaDEP1 protein (an atypical Gγ subunit). Significantly, we discover that TaCOLD1 and mTaCOLD1 (M187K) can interfere with the physical association between TaGα‐7A and TaDEP1. Together, this study reveals that TaCOLD1 acts as a novel regulator of plant height through interfering with the formation of heterotrimeric G protein complex in bread wheat and is a valuable target for the engineering of wheat plant architecture.     

Genome‐wide association study of six quality traits reveals the association of the TaRPP13L1 gene with flour colour in Chinese bread wheat

Flour colour, kernel hardness, grain protein content and wet gluten content are important quality properties that determine end use in bread wheat. Here, a wheat 90K genotyping assay was used for a genome‐wide association study (GWAS) of the six quality‐related traits in Chinese wheat cultivars in eight environments over four years. A total of 846 significant single nucleotide polymorphisms (SNPs) were identified, explaining approximately 30% of the phenotypic variation on average, and 103 multienvironment‐significant SNPs were detected in more than four environments. Quantitative trait loci (QTL) mapping in the biparent population confirmed some important SNP loci. Moreover, it was determined that some important genes were associated with the six quality traits, including some known functional genes and annotated unknown functional genes. Of the annotated unknown functional genes, it was verified that TaRPP13L1 was associated with flour colour. Wheat cultivars or lines with TaRPP13L1‐B1a showed extremely significantly higher flour redness and lower yellowness than those with TaRPP13L1‐B1b in the Chinese wheat natural population and the doubled haploid (DH) population. Two tetraploid wheat lines with premature stop codons of the TaRPP13L1 gene mutagenized by ethyl methanesulfonate (EMS) showed extremely significantly higher flour redness and lower yellowness than wild type. Our data suggest that the TaRPP13L1 gene plays an important role in modulating wheat flour colour. This study provides useful information for further dissection of the genetic basis of flour colour and also provides valuable genes or genetic loci for marker‐assisted selection to improve the process of breeding quality wheat in China.