Genome-wide dissection of hybridization for fiber quality- and yield-related traits in upland cotton.

An evaluation of combining ability can facilitate the selection of suitable parents and superior F1 hybrids for hybrid cotton breeding, although the molecular genetic basis of combining ability has not been fully characterized. In the present study, 282 female parents were crossed with four male parents in accordance with the North Carolina II mating scheme to generate 1128 hybrids. The parental lines were genotyped based on restriction site-associated DNA sequencing and 306 814 filtered single nucleotide polymorphisms were used for genome-wide association analysis involving the phenotypes, general combining ability (GCA) values, and specific combining ability values of eight fiber quality- and yield-related traits. The main results were: (i) all parents could be clustered into five subgroups based on population structure analyses and the GCA performance of the female parents had significant differences between subgroups; (ii) 20 accessions with a top 5% GCA value for more than one trait were identified as elite parents for hybrid cotton breeding; (iii) 120 significant single nucleotide polymorphisms, clustered into 66 quantitative trait loci, such as the previously reported Gh_A07G1769 and GhHOX3 genes, were found to be significantly associated with GCA; and (iv) identified quantitative trait loci for GCA had a cumulative effect on GCA of the accessions. Overall, our results suggest that pyramiding the favorable loci for GCA may improve the efficiency of hybrid cotton breeding.

Clustering Cloud-Like Model-Based Targets Underwater Tracking for AUVs.

Autonomous underwater vehicles (AUVs) rely on a mechanically scanned imaging sonar that is fixedly mounted on AUVs for underwater target barrier-avoiding and tracking. When underwater targets cross or approach each other, AUVs sometimes fail to track, or follow the wrong target because of the incorrect association of the multi-target. Therefore, a tracking method adopting the cloud-like model data association algorithm is presented in order to track underwater multiple targets. The clustering cloud-like model (CCM) not only combines the fuzziness and randomness of the qualitative concept, but also achieves the conversion of the quantitative values. Additionally, the nearest neighbor algorithm is also involved in finding the cluster center paired to each target trajectory, and the hardware architecture of AUVs is proposed. A sea trial adopting a mechanically scanned imaging sonar fixedly mounted on an AUV is carried out in order to verify the effectiveness of the proposed algorithm. Experiment results demonstrate that compared with the joint probabilistic data association (JPDA) and near neighbor data association (NNDA) algorithms, the new algorithm has the characteristic of more accurate clustering.

Integration of conventional and advanced molecular tools to track footprints of heterosis in cotton.

BACKGROUND: Heterosis, a multigenic complex trait extrapolated as sum total of many phenotypic features, is widely utilized phenomenon in agricultural crops for about a century. It is mainly focused on establishing vigorous cultivars with the fact that its deployment in crops necessitates the perspective of genomic impressions on prior selection for metric traits. In spite of extensive investigations, the actual mysterious genetic basis of heterosis is yet to unravel. Contemporary crop breeding is aimed at enhanced crop production overcoming former achievements. Leading cotton improvement programs remained handicapped to attain significant accomplishments. RESULTS: In mentioned context, a comprehensive project was designed involving a large collection of cotton accessions including 284 lines, 5 testers along with their respective F1 hybrids derived from Line × Tester mating design were evaluated under 10 diverse environments. Heterosis, GCA and SCA were estimated from morphological and fiber quality traits by L × T analysis. For the exploration of elite marker alleles related to heterosis and to provide the material carrying such multiple alleles the mentioned three dependent variables along with trait phenotype values were executed for association study aided by microsatellites in mixed linear model based on population structure and linkage disequilibrium analysis. Highly significant 46 microsatellites were discovered in association with the fiber and yield related traits under study. It was observed that two-thirds of the highly significant associated microsatellites related to fiber quality were distributed on D sub-genome, including some with pleiotropic effect. Newly discovered 32 hQTLs related to fiber quality traits are one of prominent findings from current study. A set of 96 exclusively favorable alleles were discovered and C tester (A971Bt) posited a major contributor of these alleles primarily associated with fiber quality. CONCLUSIONS: Hence, to uncover hidden facts lying within heterosis phenomenon, discovery of additional hQTLs is required to improve fibre quality. To grab prominent improvement in influenced fiber quality and yield traits, we suggest the A971 Bt cotton cultivar as fundamental element in advance breeding programs as a parent of choice.

Adaptive Kalman Filter-Based Single-Beacon Underwater Tracking with Unknown Effective Sound Velocity.

In the single-beacon underwater tracking system, vehicles rely on slant range measurements from an acoustic beacon to bound errors accumulated by dead reckoning. Ranges are usually obtained based on a presumed known effective sound velocity (ESV). Since the ESV is difficult to determine accurately, traditional methods suffer from large positioning error. By treating the unknown ESV as a state variable, a novel single-beacon tracking model (the so called "5-sv" model) and an extended Kalman filter (EKF)-based solution method have been discussed to solve the problem of ESV estimation. However, due to the uncertainty of underwater acoustic propagation, the probabilistic characteristics of the ESV uncertainty and acoustic measurement noise are unknown and varying both with time and location. EKF, which runs with presupposed noise parameters, cannot describe the practical noise specifications. To overcome the divergence issue of EKF-based single-beacon tracking methods, this paper proposes an adaptive Kalman filter-based single-beacon tracking algorithm which employs the "5-sv" model as the baseline model. Through numerical examples using simulated and field data, both the filter and smoother results show that while implementing the proposed algorithm, the tracking accuracy can be significantly improved, and the estimated noise parameter agrees well with its true value.

Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.).

Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China. Three subpopulations were found after the estimation of population structure. The pair-wise kinship values varied from 0 to 0.867. Only 1.59% of the total marker locus pairs showed significant linkage disequilibrium (LD, p < 0.001). The genome-wide LD decayed within the genetic distance of ~30 to 32 cM at r 2 = 0.1, and decreased to ~1 to 2 cM at r 2 = 0.2, indicating the potential for association mapping. Analysis based on a mixed linear model detected 57 significant (p < 0.01) marker-trait associations, including seven associations for fiber length, ten for fiber micronaire, nine for fiber strength, eight for fiber elongation, five for fiber uniformity index, five for fiber uniformity ratio, six for boll weight and seven for lint percent, for a total of 35 SSR markers, of which 11 markers were associated with more than one trait. Among marker-trait associations, 24 associations coincided with the previously reported quantitative trait loci (QTLs), the remainder were newly identified QTLs/genes. The QTLs identified in this study will potentially facilitate improvement of fiber yield and quality in the future cotton molecular breeding programs.

Full prescribed performance trajectory tracking control strategy of autonomous underwater vehicle with disturbance observer.

This paper investigates trajectory tracking control of the Autonomous Underwater Vehicle (AUV) with the general uncertainty consisting of model uncertainties and unknown ocean current disturbances. A full prescribed performance control strategy based on disturbance observer is developed, which ensures that the tracking error, the velocity error, and the observation error are all constrained. First, under the case of unmeasurable AUV acceleration, a fixed-time observer is constructed to estimate the general uncertainty, which constrains the observation error within the prescribed accuracy by a prescribed performance observer. Then, based on the performance function and corresponding error transformation, a prescribed performance protocol is designed to realize the trajectory tracking control, so that the observation error, the tracking error, and the velocity error are all constrained within the prescribed accuracy range. Simulation results demonstrate the efficiency of the full prescribed performance control strategy while the AUV tracking control with full state constraints is feasible. Moreover, compared with the other two relevant works, this study improves the observation performance by at least 10 %, both in case of deepwater disturbances and near-surface disturbances.

Hydrodynamic analysis and manipulation control on a streamlined I-AUV.

Hydrodynamics analysis and control are very significant for the seabed operations, particularly for the intelligent manipulation process of streamlined intervention autonomous underwater vehicles (I-AUVs). The computation fluid dynamics simulations and verification were conducted in the consideration with water channel domain, mesh insensitivity, support straight bar connector, free surface and other boundary conditions. The variation trend of hydrodynamic coefficients in the process of manipulation is obtained, by simulations of streamlined I-AUV manipulation under dynamic manipulation state. To further realize underwater floating manipulation, a novel controller with an integral termed nonlinear sliding mode surface and disturbance observer has been developed. The disturbance observer can make quantity analysis on the interaction forces between I-AUV and the environment from hydrodynamic analysis. Simulations and experiments have verified the controller performance.

An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations.

Construction and improvement of a genetic map for peanut (Arachis hypogaea L.) continues to be an important task in order to facilitate quantitative trait locus (QTL) analysis and the development of tools for marker-assisted breeding. The objective of this study was to develop a comparative integrated map from two cultivated × cultivated recombinant inbred line (RIL) mapping populations and to apply in mapping Tomato spotted wilt virus (TSWV) resistance trait in peanut. A total of 4,576 simple sequence repeat (SSR) markers from three sources: published SSR markers, newly developed SSR markers from expressed sequence tags (EST) and from bacterial artificial chromosome end-sequences were used for screening polymorphisms. Two cleaved amplified polymorphic sequence markers were also included to differentiate ahFAD2A alleles and ahFAD2B alleles. A total of 324 markers were anchored on this integrated map covering 1,352.1 cM with 21 linkage groups (LGs). Combining information from duplicated loci between LGs and comparing with published diploid maps, seven homoeologous groups were defined and 17 LGs (A1-A10, B1-B4, B7, B8, and B9) were aligned to corresponding A-subgenome or B-subgenome of diploid progenitors. One reciprocal translocation was confirmed in the tetraploid-cultivated peanut genome. Several chromosomal rearrangements were observed by comparing with published cultivated peanut maps. High consistency with cultivated peanut maps derived from different populations may support this integrated map as a reliable reference map for peanut whole genome sequencing assembling. Further two major QTLs for TSWV resistance were identified for each RILs, which illustrated the application of this map.

Fault-tolerant trajectory tracking control for unmanned surface vehicle with actuator faults based on a fast fixed-time system.

In this paper, an observer-based fixed-time tracking control strategy is presented for unmanned surface vehicles (USVs) with model uncertainties, external disturbances, and actuator faults. Firstly, as the theory foundation, a fast fixed-time stable system that has a shorter settling time than the existing systems is proposed. According to this system and the motion characteristics of an USV, a fast fixed-time disturbance observer is developed to obtain the unknown effects caused by lumped uncertainties. By combining the estimated knowledge and a nonsingular fast fixed-time terminal sliding surface, a robust fast fixed-time trajectory tracking controller is designed for the USV. According to Lyapunov stability theory, the fast fixed-time convergence of the proposed controller is proved. Finally, the simulation results demonstrate the effectiveness of the developed control scheme.

Hydrodynamic performance optimization and experimental verification of underwater glider based on parametric method.

In this paper, the wing body fusion method is used to complete the design of underwater glider. On this basis, the traditional optimization algorithm of underwater gliding wing shape is improved. Based on the improved Hicks Henne algorithm and genetic algorithm, the shape optimization of underwater glider is completed. Through the further optimization of the overall performance, the overall shape of the glider is improved and the maximum lift drag ratio is increased. Finally, the physical experiment of the optimized shape is carried out according to the experimental water area of the circulating water tank. Through the comparative analysis of the data, the accuracy of the numerical calculation is verified.

Mapping of epistatic quantitative trait loci in four-way crosses.

Four-way crosses (4WC) involving four different inbred lines often appear in plant and animal commercial breeding programs. Direct mapping of quantitative trait loci (QTL) in these commercial populations is both economical and practical. However, the existing statistical methods for mapping QTL in a 4WC population are built on the single-QTL genetic model. This simple genetic model fails to take into account QTL interactions, which play an important role in the genetic architecture of complex traits. In this paper, therefore, we attempted to develop a statistical method to detect epistatic QTL in 4WC population. Conditional probabilities of QTL genotypes, computed by the multi-point single locus method, were used to sample the genotypes of all putative QTL in the entire genome. The sampled genotypes were used to construct the design matrix for QTL effects. All QTL effects, including main and epistatic effects, were simultaneously estimated by the penalized maximum likelihood method. The proposed method was confirmed by a series of Monte Carlo simulation studies and real data analysis of cotton. The new method will provide novel tools for the genetic dissection of complex traits, construction of QTL networks, and analysis of heterosis.

GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton (Gossypium hirsutum L.) Across Multiple Environments.

For about a century, plant breeding has widely exploited the heterosis phenomenon-often considered as hybrid vigor-to increase agricultural productivity. The ensuing F1 hybrids can substantially outperform their progenitors due to heterozygous combinations that mitigate deleterious mutations occurring in each genome. However, only fragmented knowledge is available concerning the underlying genes and processes that foster heterosis. Although cotton is among the highly valued crops, its improvement programs that involve the exploitation of heterosis are still limited in terms of significant accomplishments to make it broadly applicable in different agro-ecological zones. Here, F1 hybrids were derived from mating a diverse Upland Cotton germplasm with commercially valuable cultivars in the Line × Tester fashion and evaluated across multiple environments for 10 measurable traits. These traits were dissected into five different heterosis types and specific combining ability (SCA). Subsequent genome-wide predictions along-with association analyses uncovered a set of 298 highly significant key single nucleotide polymorphisms (SNPs)/Quantitative Trait Nucleotides (QTNs) and 271 heterotic Quantitative Trait Nucleotides (hQTNs) related to agronomic and fiber quality traits. The integration of a genome wide association study with RNA-sequence analysis yielded 275 candidate genes in the vicinity of key SNPs/QTNs. Fiber micronaire (MIC) and lint percentage (LP) had the maximum number of associated genes, i.e., each with 45 related to QTNs/hQTNs. A total of 54 putative candidate genes were identified in association with HETEROSIS of quoted traits. The novel players in the heterosis mechanism highlighted in this study may prove to be scientifically and biologically important for cotton biologists, and for those breeders engaged in cotton fiber and yield improvement programs.

Distributed tracking control for multiple Euler-Lagrange systems with communication delays and input saturation.

This study mainly investigates the problem of distributed tracking control for time-varying delay existing multiple Euler-Lagrange systems considering full-state constraints and input saturation under the directed graph. Specifically, the system under consideration consists of system uncertainties and external disturbances. In the control law design, a distributed observer is first designed that the followers can obtain the leader's time-varying information. Then the barrier Lyapunov function technique is used to make sure the system errors can converge to a certain range while the anti-windup method is utilized to overcome the influence of control input saturation. Further, in order to prevent chattering, an adaptive law is given. Numerical simulations are given to verify the proposed algorithms.

Computational fluid dynamics approaches to drag and wake of a long-line mussel dropper under tidal current.

Hydrodynamic effects of mussel farms have attracted increased research attentions in recent years. The understanding of the hydrodynamic impacts is essential for predicting the sustainability of mussel farms. A large mussel farm includes thousands of mussel droppers, and the combined drag on the mussel droppers is sufficient to possibly affect the longevity of the entire long-lines. This article intends to study the drag and wake of an individual long-line mussel dropper using computational fluid dynamics approaches. Two equivalent rough cylinders, namely, Curved-Model and Sharp-Model, have been utilized to simulate the mussel dropper, and each rough cylinder is assigned with surface roughness. The porosity is not considered in this article due to its complexity from inhalant and exhalant of mussels. Two-dimensional laminar simulations are conducted at Reynolds number from 10 to 200, and three-dimensional large eddy simulations are conducted at subcritical Reynolds number ranging from 3900 to 105. The results show that larger drag coefficients and Strouhal numbers are attributed to surface roughness and sharp crowns on the rough cylinder. The obtained drag coefficient ranges from 1.1 to 1.2 with respect to the diameter of the mussel dropper and the peak value of the tidal velocities. Wakes behind rough cylinders fluctuate more actively compared to those of smooth cylinders. This research work provides new insight for further investigations on hydrodynamic interactions between fluid and mussel droppers.

Identification of associated SSR markers for yield component and fiber quality traits based on frame map and Upland cotton collections.

Detecting QTLs (quantitative trait loci) that enhance cotton yield and fiber quality traits and accelerate breeding has been the focus of many cotton breeders. In the present study, 359 SSR (simple sequence repeat) markers were used for the association mapping of 241 Upland cotton collections. A total of 333 markers, representing 733 polymorphic loci, were detected. The average linkage disequilibrium (LD) decay distances were 8.58 cM (r2 > 0.1) and 5.76 cM (r2 > 0.2). 241 collections were arranged into two subgroups using STRUCTURE software. Mixed linear modeling (MLM) methods (with population structure (Q) and relative kinship matrix (K)) were applied to analyze four phenotypic datasets obtained from four environments (two different locations and two years). Forty-six markers associated with the number of bolls per plant (NB), boll weight (BW), lint percentage (LP), fiber length (FL), fiber strength (FS) and fiber micornaire value (FM) were repeatedly detected in at least two environments. Of 46 associated markers, 32 were identified as new association markers, and 14 had been previously reported in the literature. Nine association markers were near QTLs (at a distance of less than 1-2 LD decay on the reference map) that had been previously described. These results provide new useful markers for marker-assisted selection in breeding programs and new insights for understanding the genetic basis of Upland cotton yields and fiber quality traits at the whole-genome level.

Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes.

The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)(4×), were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.

An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.).

Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01-a10 and b01-b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut.

QTL mapping of yield and fiber traits based on a four-way cross population in Gossypium hirsutum L.

Four-way cross (4WC) involving four different inbred lines frequently appears in the cotton breeding programs. However, linkage analysis and quantitative trait loci (QTL) mapping with molecular markers in cotton has largely been applied to populations derived from a cross between two inbred lines, and few results of QTL dissection were conducted in a 4WC population. In this study, an attempt was made to construct a linkage map and identify QTL for yield and fiber quality traits in 4WC derived from four different inbred lines in Gossypium hirsutum L. A linkage map was constructed with 285 SSR loci and one morphological locus, covering 2113.3 cM, approximately 42% of the total recombination length of the cotton genome. A total of 31 QTL with 5.1-25.8% of the total phenotypic variance explained were detected. Twenty-four common QTL across environments showed high stability, and six QTL were environment-specific. Several genomic segments affecting multiple traits were identified. The advantage of QTL mapping using a 4WC were discussed. This study presents the first example of QTL mapping using a 4WC population in upland cotton. The results presented here will enhance the understanding of the genetic basis of yield and fiber quality traits and enable further marker-assisted selection in cultivar populations in upland cotton.