Evaluation on Potential Risk of the Emerging Yr5-Virulent Races of Puccinia striiformis f. sp. tritici to 165 Chinese Wheat Cultivars

In 2017, a new race (TSA-6) of the wheat stripe rust pathogen, Puccinia striiformis f. sp. tritici, virulent to resistance gene Yr5 were detected in China. However, whether Chinese wheat cultivars are resistant to the new races was unknown. In this study, two isolates (TSA-6 and TSA-9) with virulence to Yr5 were tested on other wheat Yr gene lines for their avirulence/virulence patterns and used, together with prevalent races CYR32 and CYR34 without the Yr5 virulence, to evaluate 165 major Chinese wheat cultivars for their reactions. Isolates TSA-6 and TSA-9 had similar but different virulence spectra, and therefore should be considered as two different races. Their avirulent/virulence patterns were remarkably different from that of CYR34 but quite similar to that of CYR32. Of the 165 wheat cultivars, 21 had all-stage resistance to TSA-6, 34 to TSA-9, and 20 to both races. Adult-plant resistance (APR) was detected in 35 cultivars to TSA-6 and 27 to TSA-9, but only 3 cultivars showed APR to both new races. Slow rusting resistance was observed in 24 cultivars to TSA-6 and of 33 to TSA-9. Analysis of variance (ANOVA) of disease index indicated a significant difference among cultivars, but not among the four races. Based on the molecular marker data, a low percentage of wheat cultivars carried Yr5, Yr7, Yr10, Yr15, Yr26, and/or YrSP. As TSA-6 and TSA-9 can be a serious threat to wheat production in China, monitoring TSA-6, TSA-9, and other races are continually needed.

Kennard-Stone method outperforms the Random Sampling in the selection of calibration samples in SNPs and NIR data

ABSTRACT: Splitting the whole dataset into training and testing subsets is a crucial part of optimizing models. This study evaluated the influence of the choice of the training subset in the construction of predictive models, as well as on their validation. For this purpose we assessed the Kennard-Stone (KS) and the Random Sampling (RS) methods in near-infrared spectroscopy data (NIR) and marker data SNPs (Single Nucleotide Polymorphisms). It is worth noting that in SNPs data, there is no knowledge of reports in the literature regarding the use of the KS method. For the construction and validation of the models, the partial least squares (PLS) estimation method and the Bayesian Lasso (BLASSO) proved to be more efficient for NIR data and for marker data SNPs, respectively. The evaluation of the predictive capacity of the models obtained after the data partition occurred through the correlation between the predicted and the observed values, and the corresponding square root of the mean squared error of prediction. For both datasets, results indicated that the results from KS and RS methods differ statistically from each other by the F test (P-value < 0.01). The KS method showed to be more efficient than RS in practically all repetitions. Also, KS method has the advantage of being easy and fast to be applied and also to select the same samples, which provides excellent benefits in the following analyses.

KONSEP ILMU PENGETAHUAN LOKAL DALAM LEKSIKON PENANDA WAKTU DAN MUSIM SUKU DAYAK MERATUS [The Indigenous Knowledge Science Lexicon Marking the Time and Season of the Meratus Dayak Tribe]

This study aims to describe the indigenous science in the lexicon of time and season markers by the Meratus Dayak tribe. The method used in this research is descriptive qualitative ethnolinguistic approach. The data in this study are lexicon markers of time and season spoken by the Meratus Dayak tribe who reside in the Balangan Regency, namely Meratus Balangan Dayak, especially traditional leader and balian. Meanwhile the data collection techniques used were participant observation, listening techniques, and record techniques. Data analysis includes: (1) transcribing data obtained through the results of records and records; (2) identifying time and season marker data; (3) classifying data according to lingual form and lexicon function; and (4) analyze and conclude. Based on the results of the analysis it was found that the concept of local science in the lexicon markers of time and season can be classified into two: (1) based on the lingual form and (2) based on the function of the lexicon. The concept of local science is based in the lingual form: first, the lexicon marking the time and season of tangible words which a total of 30 lexicons. Second, lexicons marking the time and season in the form of phrases that include noun caterogical phrases, verb categorized phrases, and numeralia categorized phrases with a total of 21 lexicons. Then, the concept of local science based on the function of the lexicon, among others: (1) the function of the daily time lexicon is as much as 19 lexicon and (2) the time and season lexicon functions with a larger unit of 20 lexicon. Penelitian ini bertujuan mendeskripsikan konsep ilmu pengetahuan lokal dalam leksikon penanda waktu dan musim oleh suku Dayak Meratus. Metode yang digunakan dalam penelitian ini adalah deskriptif kualitatif dengan pendekatan etnolinguistik. Data dalam penelitian ini berupa leksikon penanda waktu dan musim yang dituturkan oleh suku Dayak Meratus yang bertempat tinggal di wilayah Kabupaten Balangan, yakni Dayak Meratus Balangan, terutama tokoh adat dan balian. Adapun, teknik pengumpulan data yang digunakan adalah observasi partisipan, teknik simak, dan teknik rekam. Analisis data meliputi: (1) mentranskripsikan data yang diperoleh melalui hasil catatan dan rekaman; (2) mengidentifikasi data penanda waktu dan musim; (3) mengklasifikasikan data sesuai dengan bentuk lingual dan fungsi leksikon; dan (4) menganalisis dan menyimpulkan. Berdasarkan hasil analisis ditemukan bahwa konsep ilmu pengetahuan lokal dalam leksikon penanda waktu dan musim dapat diklasifikasikan menjadi dua: (1) berdasarkan bentuk lingual dan (2) berdasarkan fungsi leksikon. Konsep ilmu pengetahuan lokal berdasarkan bentuk lingual: pertama, leksikon penanda waktu dan musim berwujud kata yang meliputi nomina, verba, dan numeralia dengan jumlah keseluruhan 30 leksikon. Kedua, leksikon penanda waktu dan musim berwujud frasa yang meliputi frasa berkategori nomina, frasa berkategori verba, dan frasa berkategori numeralia dengan jumlah keseluruhan 21 leksikon. Kemudian, konsep ilmu pengetahuan lokal berdasarkan fungsi leksikon, antara lain: (1) fungsi leksikon penanda waktu harian sebanyak 19 leksikon dan (2) fungsi leksikon penanda waktu dan musim dengan satuan yang lebih besar sebanyak 20 leksikon.

A generic hidden Markov model for multi-parent populations

A common step in the analysis of multi-parent populations is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a probability model for the pattern of founder alleles along chromosomes, including the relative frequency of founder alleles and the probability of exchanges among them, which depend on a model for meiotic recombination and on the mating design for the population. While the precise experimental design used to generate the population may be used to derive a precise characterization of the model for exchanges among founder alleles, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of multi-parent populations. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly-available data on Diversity Outbred and Collaborative Cross mice.

PSVIII-2 Genetic diversity analysis of hybrid Karachaev goats (Capra hircus) population using microsatellite marker data

The Karachaev goat is an indigenous breed that possesses unique features including significantly less fat deposition in the body compared to sheep and cattle, ability to graze at an altitude of up to 1200 meters and to produce fertile hybrids with wild relatives. To understand the genetic diversity and population structure of hybrids between domestic Karachaev goats (Capra hircus) and The West Caucasian tur (Capra caucasica) 143 individuals were analyzed using 10 microsatellites panel. Sample were analyzed according to the manufacturer’s recommendations on an automatic sequencer, ABI 3130XL genetic analyzer (Applied Biosystems). Genetic diversity was calculated using GenAlEx 6.503 software. Genotyping of ten microsatellite loci in hybrid forms of Karachaev goats and turs detected 106 alleles in total. Na values ranged from five (INR063) to seventeen (SRCRSO008), averaging 10.6 alleles per locus across the 10 loci. All loci were polymorphic. The average number of alleles was 10.6 alleles per locus. This is higher than the similar indicator obtained by Kharzinova et al. (2019) in populations of Soviet wool, Tajik wool, Orenburg downy, Alpine and Zaanen dairy breeds of goats, studied using the panel of same 10 STR-markers (9.3 loci). Other key indexes of genetic diversity could be found in table 1. The values of the coefficient FIS suggest the absence of related mating in the herd. Information on genotypic variability of Karachaev goats hybrid forms obtained here will contribute into the breeding programs improvement and to preservation of existing native breeds.

Assessing the validity of dual-minima algorithm for heel-strike and toe-off prediction for the amputee population

Assessment of gait deficits relies on accurate gait segmentation based on the key gait events of heel strike (HS) and toe-off (TO). Kinematics-based estimation of gait events has shown promise in this regard especially using the leg velocity signal and gyroscopic sensors. However, its validation for the amputee population is not established in the literature. The goal of this study is to assess the accuracy of lower-leg angular velocity signal in determining the TO and HS instants for the amputee population. An open data set containing marker data of 10 subjects with unilateral transfemoral amputation during treadmill walking was used. A rule-based dual-minima algorithm was developed to detect the landmarks in the shank velocity signal indicating TO and HS events. The predictions were compared against the force platform data for 2595 walking cycles from 239 walking trials. Results showed considerable accuracy for the HS with a median error of -1ms. The TO prediction error was larger with the median ranging from 35-84ms. The algorithm consistently predicted the TO earlier than the actual event. Significant differences were found between the prediction accuracy for the sound and prosthetic legs. The prediction accuracy was also affected by the subjects’ mobility level (K-level) but was largely unaffected by gait speed. In conclusion, the leg velocity profile during walking can predict the heel-strike and toe-off events for the transfemoral amputee population with varying degrees of accuracy depending upon the leg side and amputee’s functional ability level.

A general hidden Markov model for multi-parent populations

A common step in the analysis of multi-parent populations is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a model for the exchange process along chromosomes, including the relative frequency of founder alleles and of the probability of exchanges among them. While the precise experimental design used to generate the population may be used to derive a precise characterization of the exchange process, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of multi-parent populations. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly available data on Diversity Outbred and Collaborative Cross mice.

Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm

The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.

A marker registration method to improve joint angles computed by constrained inverse kinematics

Accurate computation of joint angles from optical marker data using inverse kinematics methods requires that the locations of markers on a model match the locations of experimental markers on participants. Marker registration is the process of positioning the model markers so that they match the locations of the experimental markers. Markers are typically registered using a graphical user interface (GUI), but this method is subjective and may introduce errors and uncertainty to the calculated joint angles and moments. In this investigation, we use OpenSim to isolate and quantify marker registration–based error from other sources of error by analyzing the gait of a bipedal humanoid robot for which segment geometry, mass properties, and joint angles are known. We then propose a marker registration method that is informed by the orientation of anatomical reference frames derived from surface-mounted optical markers as an alternative to user registration using a GUI. The proposed orientation registration method reduced the average root-mean-square error in both joint angles and joint moments by 67% compared to the user registration method, and eliminated variability among users. Our results show that a systematic method for marker registration that reduces subjective user input can make marker registration more accurate and repeatable.