Inclusive Mapping Research Articles

Enhanced stripe rust resistance obtained by combining Yr30 with a widely dispersed, consistent QTL on chromosome arm 4BL.

YrFDC12 and PbcFDC, co-segregated in chromosome 4BL, and significantly interacted with Yr30/Pbc1 to enhance stripe rust resistance and to promote pseudo-black chaff development. Cultivars with durable resistance are the most popular means to control wheat stripe rust. Durable resistance can be achieved by stacking multiple adult plant resistance (APR) genes that individually have relatively small effect. Chinese wheat cultivars Ruihua 520 (RH520) and Fengdecun 12 (FDC12) confer partial APR to stripe rust across environments. One hundred and seventy recombinant inbred lines from the cross RH520 × FDC12 were used to determine the genetic basis of resistance and identify genomic regions associated with stripe rust resistance. Genotyping was carried out using 55K SNP array, and eight quantitative trait loci (QTL) were detected on chromosome arms 2AL, 2DS, 3BS, 4BL, 5BL (2), and 7BL (2) by inclusive composite interval mapping. Only QYr.nwafu-3BS from RH520 and QYr.nwafu-4BL.2 (named YrFDC12 for convenience) from FDC12 were consistent across the four testing environments. QYr.nwafu-3BS is likely the pleiotropic resistance gene Sr2/Yr30. YrFDC12 was mapped in a 2.1-cM interval corresponding to 12Mb and flanked by SNP markers AX-111121224 and AX-89518393. Lines harboring both Yr30 and YrFDC12 displayed higher resistance than the parents and expressed pseudo-black chaff (PBC) controlled by loci Pbc1 and PbcFDC12, which co-segregated with Yr30 and YrFDC12, respectively. Both marker-based and pedigree-based kinship analyses revealed that YrFDC12 was inherited from founder parent Zhou 8425B. Fifty-four other wheat cultivars shared the YrFDC12 haplotype. These results suggest an effective pyramiding strategy to acquire highly effective, durable stripe rust resistance in breeding.

Mapping of QTL for agronomic traits using high-density SNPs with an RIL population in maize.

Genome wide association studies (GWAS) have been widely used to identify QTLs underlying quantitative traits in humans and animals, and they have also become a popular method of mapping QTLs in many crops, including maize. Advances in high-throughput genotyping technologies enable construction of high-density linkage maps using SNP markers. High-density genetic mapping must precede to find molecular markers associated with a particular trait. The objectives of this study were to (1) construct a high-density linkage map using SNP markers and (2) detect the QTLs for grain yield and quality related traits of the Mo17/KW7 RIL population. In this study, two parental lines, Mo17 (normal maize inbred line) and KW7 (waxy inbred line) and 80 F7:8 lines in the Mo17/KW7 RIL population were genotyped using the MaizeSNP50 BeadChip, an Illumina BeadChip array of 56,110 maize SNPs. Marker integration and detection of QTLs was performed using the inclusive composite interval mapping (ICIM) method within the QTL IciMapping software. This study was genotyped using the Illumina MaizeSNP50 BeadChip for maize Mo17/KW7 recombinant inbred line (RIL) population. The 2904 SNP markers were distributed along all 10 maize chromosomes. The total length of the linkage map was 3553.7cm, with an average interval of 1.22cm between SNPs. A total of 18 QTLs controlling eight traits were detected in the Mo17/KW7 RIL population. Three QTLs for plant height (PH) were detected on chromosomes 4 and 8 and showed from 16.01% (qPH8) to 19.85% (qPH4a) of phenotypic variance. Five QTLs related to ear height (EH) were identified on chromosomes 3, 4, and 6 and accounted for 3.79% (qEH6) to 27.57% (qEH4b) of phenotypic variance. Five QTLs related to water content (WC) on chromosomes 1, 4, 8, and 9 accounted for 9.55% (qWC8b) to 23.30% (qWC4) of phenotypic variance. One QTL (qAC9) relating to amylose content (AC) on chromosome 9 showed 82.10% of phenotypic variance. The high-density linkage map and putative QTLs of the maize RIL population detected in this study can be effectively utilized in waxy and normal maize breeding programs to facilitate the selection process through marker-assisted selection (MAS) breeding programs.

CULTURAL-RECREATIONAL TOURIST CHERKASY REGION: INCLUSIVE-SOCIAL 3D-MAPS (from the work of Pavlo Tychyna Uman State Pedagogical University)

The article analyzes the peculiarities of tourism development in the Cherkasy region in a pandemic. New technological opportunities for cultural leisure and knowledge of the historical and cultural heritage of the region are considered. The experience of Pavlo Tychyna Uman State Pedagogical University project implementation is analyzed inclusive-social 3D-map. It is noted that the 3D map will help provide equal opportunities for people with disabilities in terms of tourism.
 It has been given that the development of information and communication technologies also largely determines the social transformation «Cultural, recreational and tourist Cherkasy region: inclusive and social 3D-map». It will offer ways to solve the problem of education and social development of people with disabilities, creating new technologies to improve quality of life. , the introduction of an effective system of social and psychological rehabilitation of children and youth with special educational needs through culture and inclusive tourism.
 International experience of the implementation of the virtual tour convincingly proves that this area of activity creates conditions for improving the competitiveness of tourist services. Such a tourist product, which is presented in the form of a virtual tour, is «information-intensive», more presentable and attractive. Creating an inclusive social 3D map will allow you to meet your cultural needs and demonstrate the cultural diversity of the region, which will be a reason to visit these places offline, taking into account their physical characteristics. It will expand their horizons and deepen knowledge, education of a true citizen, the formation of cognitive interest in the studied subjects, the emergence of motivation to learn, raising awareness of Ukrainians of the historical and cultural heritage of the Motherland for schoolchildren.

The Nehari manifold for indefinite Kirchhoff problem with Caffarelli-Kohn-Nirenberg type critical growth

In this paper we study the following class of nonlocal problem involving Caffarelli-Kohn-Nirenberg type critical growth $$ L(u)-\lambda h(x)|x|^{-2(1+a)}u=\mu f(x)|u|^{q-2}u+|x|^{-pb}|u|^{p-2}u\quad \text{in } \mathbb R^N, $$% where $h(x)\geq 0$, $f(x)$ is a continuous function which may change sign, $\lambda, \mu$ are positive real parameters and $1< q< 2< 4< p=2N/[N+2(b-a)-2]$, $0\leq a< b< a+1< N/2$, $N\geq 3$. Here $$ L(u)=-M\left(\int_{\mathbb R^N} |x|^{-2a}|\nabla u|^2dx\right)\mathrm {div} \big(|x|^{-2a}\nabla u\big) $$ and the function $M\colon \mathbb R^+_0\to\mathbb R^+_0$ is exactly the Kirchhoff model, given by $M(t)=\alpha+\beta t$, $\alpha, \beta> 0$. The above problem has a double lack of compactness, firstly because of the non-compactness of Caffarelli-Kohn-Nirenberg embedding and secondly due to the non-compactness of the inclusion map $$u\mapsto \int_{\mathbb R^N}h(x)|x|^{-2(a+1)}|u|^2dx,$$ as the domain of the problem in consideration is unbounded. Deriving these crucial compactness results combined with constrained minimization argument based on Nehari manifold technique, we prove the existence of at least two positive solutions for suitable choices of parameters $\lambda$ and $\mu$.

Inclusion Theorems for the Moyal Multiplier Algebras of Generalized Gelfand–Shilov Spaces

We prove that the Moyal multiplier algebras of the generalized Gelfand–Shilov spaces of type S contain Palamodov spaces of type \({\mathscr {E}}\) and the inclusion maps are continuous. We also give a direct proof that the Palamodov spaces are algebraically and topologically isomorphic to the strong duals of the spaces of convolutors for the corresponding spaces of type S. The obtained results provide a general and efficient way to describe the algebraic and continuity properties of pseudodifferential operators with symbols having an exponential or super-exponential growth at infinity.

Banking or Under-banking: Spatial Role of Financial Inclusion and Exclusion

Access to bank account is only a part of the problem when we talk of financial inclusion because several people with a bank account are not necessarily using them to deposit their savings or carry out transactions. This article makes an attempt to examine the reasons for low utilisation of banking facilities. It employs financial inclusion insights (FII) data for Indian population to find out an outcome of financial inclusion (and thus social inclusion as well) based on the usage of banking services with covariates like financial literacy, the probability that any financial service is accessible to the respondent in terms distance, type of mobile phone and spatial density. We use truncated probit model to measure the incidence of under-banking. Our findings show that there is a negative association between supply-side constraints and usage of banking services, implying that low access to financial services in time and space stands as a hindrance to financial inclusion. Further, we find from the financial inclusion and exclusion map at the district level that even though economic agents intend to participate in the space in which he/she is living is not much inclusive.

Finite-time stabilization of memristor-based inertial neural networks with time-varying delays combined with interval matrix method

This paper investigates the finite-time stability problem of memristor-based inertial neural networks (MINNs) with time-varying delays in association with the interval matrix approach. In the light of differential inclusion and set-valued mapping, the delayed MINNs are converted to a category of systems with uncertain terms by means of convex combination transformations of matrices to deal with the problem of the parameter mismatch of MINNs. Afterwards, the second-order differential systems are simplified to the ordinary first-order differential systems utilizing dimension reduction. Then, two types of delayed feedback controllers are designed to ensure that MINNs can achieve finite-time stabilization, which handles time-varying delays in different ways. Meanwhile, the finite-time stabilization criterion can be deduced by linear matrix inequalities (LMIs). Therefore, the upper bound on the settling time is estimated as one of the indicators to measure the stability effect. Finally, the accuracy of the theoretical results and the validity of the proposed method are verified by two examples.

QTL Mapping and Validation for Kernel Area and Circumference in Common Wheat via High-Density SNP-Based Genotyping.

As an important component, 1,000 kernel weight (TKW) plays a significant role in the formation of yield traits of wheat. Kernel size is significantly positively correlated to TKW. Although numerous loci for kernel size in wheat have been reported, our knowledge on loci for kernel area (KA) and kernel circumference (KC) remains limited. In the present study, a recombinant inbred lines (RIL) population containing 371 lines genotyped using the Wheat55K SNP array was used to map quantitative trait loci (QTLs) controlling the KA and KC in multiple environments. A total of 54 and 44 QTLs were mapped by using the biparental population or multienvironment trial module of the inclusive composite interval mapping method, respectively. Twenty-two QTLs were considered major QTLs. BLAST analysis showed that major and stable QTLs QKc.sau-6A.1 (23.12–31.64 cM on 6A) for KC and QKa.sau-6A.2 (66.00–66.57 cM on 6A) for KA were likely novel QTLs, which explained 22.25 and 20.34% of the phenotypic variation on average in the 3 year experiments, respectively. Two Kompetitive allele-specific PCR (KASP) markers, KASP-AX-109894590 and KASP-AX-109380327, were developed and tightly linked to QKc.sau-6A.1 and QKa.sau-6A.2, respectively, and the genetic effects of the different genotypes in the RIL population were successfully confirmed. Furthermore, in the interval where QKa.sau-6A.2 was located on Chinese Spring and T. Turgidum ssp. dicoccoides reference genomes, only 11 genes were found. In addition, digenic epistatic QTLs also showed a significant influence on KC and KA. Altogether, the results revealed the genetic basis of KA and KC and will be useful for the marker-assisted selection of lines with different kernel sizes, laying the foundation for the fine mapping and cloning of the gene(s) underlying the stable QTLs detected in this study.

Mapping resistance to WBNV through CIM, JICIM and QTL-meta analysis approaches in watermelon

Since past three decades, tospoviruses have been impacting severe economic losses causing heavy yield reduction in many crops. Watermelon bud necrosis disease caused by watermelon bud necrosis orthotospovirus (WBNV) is one such tospovirus that has emerged as a devastating disease of watermelon in India. Efforts are underway to develop resistant varieties at ICAR-IIHR and in the current study, efforts have been made to integrate WBNV resistance QTLs from wide range of populations and screening experiments for a comprehensive analysis through QTL-meta-analysis and joint inclusive composite interval mapping (JICIM). Comprehensive analyses for QTLs suggested MQTL_WBNV_2.1 on Chromosome 2, MQTL_WBNV_3.2 on Chromosome 3 and MQTL_WBNV_7.2 on Chromosome 7 as potential candidate QTL regions for WBNV resistance. The genes identified in these QTLs viz., Cla020173 encoding PR-1, Cla001733 encoding pathogenesis-related transcriptional factor and ethylene-responsive transcription (ERF), Cla001590 and Cla001591 genes encoding acid phosphatase, Cla019476 encoding TIR-NBS and Cla011771 belonging to TIR-NBS-LRR gene family may be investigated as putative candidates for WBNV resistance in watermelon. The results obtained in present study may provide way for functional validation of putative candidates and development of suitable markers for marker assisted selection (MAS) of WBNV resistance in watermelon.

Phenotypic performance and associated QTL of ‘Peace’ × ‘CDC Stanley’ mapping population under conventional and organic management systems

AbstractIdentification of consistent QTL in both conventional and organic management systems is a prerequisite for improving spring wheat (Triticum aestivum) through marker‐assisted selection. The objectives of the present study were to continue investigating the effect of management systems on agronomic and end‐use quality traits, and map associated quantitative trait loci (QTL) in a hard red spring wheat population. We evaluated 165 recombinant inbred lines derived from ‘Peace’ × ‘CDC Stanley’ for nine agronomic and end‐use quality traits under conventional and organic management systems for 2 yr and genotyped them with the wheat 90K iSelect array. Using inclusive composite interval mapping on phenotypic data across two environments per management and the International Wheat Genome Sequence Consortium (IWGSC) RefSeq v2.0 physical map of 1,058 informative single nucleotide polymorphisms, we uncovered 32 QTL (17 under conventional and 15 under organic) associated with nine traits of which five QTL were common in both managements. The remaining QTL were specific either to the conventional (12) or organic (10) managements. Each QTL explained from 1.2 to 19.2% and together accounted for 3.0 to 28.4% and 3.3 to 21.9% of the total phenotypic variance of each trait evaluated under conventional and organic management systems, respectively. We found three coincident genomic regions on chromosomes 1B, 3B, and 4B associated with two and three traits. All QTL identified in the present study were not reported in any of our previous mapping populations and would provide more data to wheat researchers conducting similar studies under conventional and organic management systems.

Genome-wide association screening and verification of potential genes associated with root architectural traits in maize (Zea mays L.) at multiple seedling stages

BackgroundBreeding for new maize varieties with propitious root systems has tremendous potential in improving water and nutrients use efficiency and plant adaptation under suboptimal conditions. To date, most of the previously detected root-related trait genes in maize were new without functional verification. In this study, seven seedling root architectural traits were examined at three developmental stages in a recombinant inbred line population (RIL) of 179 RILs and a genome-wide association study (GWAS) panel of 80 elite inbred maize lines through quantitative trait loci (QTL) mapping and genome-wide association study.ResultsUsing inclusive composite interval mapping, 8 QTLs accounting for 6.44–8.83 % of the phenotypic variation in root traits, were detected on chromosomes 1 (qRDWv3-1-1 and qRDW/SDWv3-1-1), 2 (qRBNv1-2-1), 4 (qSUAv1-4-1, qSUAv2-4-1, and qROVv2-4-1), and 10 (qTRLv1-10-1, qRBNv1-10-1). GWAS analysis involved three models (EMMAX, FarmCPU, and MLM) for a set of 1,490,007 high-quality single nucleotide polymorphisms (SNPs) obtained via whole genome next-generation sequencing (NGS). Overall, 53 significant SNPs with a phenotypic contribution rate ranging from 5.10 to 30.2 % and spread all over the ten maize chromosomes exhibited associations with the seven root traits. 17 SNPs were repeatedly detected from at least two growth stages, with several SNPs associated with multiple traits stably identified at all evaluated stages. Within the average linkage disequilibrium (LD) distance of 5.2 kb for the significant SNPs, 46 candidate genes harboring substantial SNPs were identified. Five potential genes viz. Zm00001d038676, Zm00001d015379, Zm00001d018496, Zm00001d050783, and Zm00001d017751 were verified for expression levels using maize accessions with extreme root branching differences from the GWAS panel and the RIL population. The results showed significantly (P < 0.001) different expression levels between the outer materials in both panels and at all considered growth stages.ConclusionsThis study provides a key reference for uncovering the complex genetic mechanism of root development and genetic enhancement of maize root system architecture, thus supporting the breeding of high-yielding maize varieties with propitious root systems.

Two decades of research on waste management in the circular economy: Insights from bibliometric, text mining, and content analyses

Achieving environmental sustainability and transition from a linear economy to a circular economy (CE) highly relies on effective waste management (WM) and how waste is treated as a potential future resource. This research aims to provide an inclusive map of the scientific background of WM in the CE context over the last two decades from 2001 to 2020 to identify its salient research themes and trends, main characteristics, evolution, and potentially valuable directions for future studies. To achieve that, the following research questions were addressed by applying a mixed-method approach including bibliometric, text mining, and content analyses: (i) how has the field of WM research evolved within the CE domain? (ii) what are the salient research themes and trends of WM in the CE? and (iii) what are the possible directions for future research on WM within the CE context? As a result, the synthesized bibliometric networks were constructed and analyzed for a total of 962 journal articles extracted from the Web of Science database to visualize the main body of literature. Consequently, the seven major research themes of WM in the CE context were identified as follows: (1) bio-based WM; (2) CE transition; (3) electronic waste; (4) municipal solid waste; (5) environmental impacts and lifecycle assessment; (6) plastic waste; and (7) construction and demolition WM. The provided inclusive research landscape of WM systems, and its prominent highlight patterns can serve as a base for a real-time guideline to lead further research areas and as a tool to support WM policy-makers and practitioners to support the CE transition (which aims to minimize the waste generation). Finally, the future research directions to better position WM research activities within the CE context as a waste minimization approach are provided.

Identification and characterization of GLOBE, a major gene controlling fruit shape and impacting fruit size and marketability in tomato

Within large-fruited germplasm, fruit size is influenced by flat and globe shapes. Whereas flat fruits are smaller and retain better marketability, globe fruits are larger and more prone to cuticle disorders. Commercial hybrids are often developed from crosses between flat and globe shaped parents because flat shape is thought to be dominant and fruit size intermediate. The objectives of this study were to determine the genetic basis of flat/globe fruit shape in large-fruited fresh-market tomato germplasm and to characterize its effects on several fruit traits. Twenty-three advanced single plant selections from the Fla. 8000 × Fla. 8111B cross were selectively genotyped using a genome-wide SNP array, and inclusive composite interval mapping identified a single locus on the upper arm of chromosome 12 associated with shape, which we termed globe. A 238-plant F2 population and 69 recombinant inbred lines for this region from the same parents delimited globe to approximately 392-kilobases. A germplasm survey representing materials from multiple breeding programs demonstrated that the locus explains the flat/globe shape broadly. A single base insertion in an exon of Solyc12g006860, a gene annotated as a brassinosteroid hydroxylase, segregated completely with shape in all populations tested. CRISPR/Cas9 knock out plants confirmed this gene as underlying the globe locus. In silico analysis of the mutant allele of GLOBE among 595 wild and domesticated accessions suggested that the allele arose very late in the domestication process. Fruit measurements in three genetic backgrounds evidenced that globe impacts fruit size and several fruit shape attributes, pedicel length/width, and susceptibility of fruit to weather check. The mutant allele of GLOBE appears mostly recessive for all traits except fruit size where it acts additively.

Analytic bundle structure on the idempotent manifold

Let X be a (real or complex) Banach space (not necessarily a Hilbert space), and $$\mathcal {I}(X)$$ be the set of all non-trivial idempotents; i.e., bounded linear operators on X whose squares equal themselves. We show that, when equipped with the Banach submanifold structure induced from $$\mathcal {L}(X)$$ , the subset $$\mathcal {I}(X)$$ is a locally trivial analytic affine-Banach bundle over the Grassmann manifold $$\mathscr {G}(X)$$ , via the map $$\kappa $$ that sends $$Q\in \mathcal {I}(X)$$ to Q(X), such that the affine-Banach space structure on each fiber is the one induced from $$\mathcal {L}(X)$$ . Using this, we show that if H is a real or complex Hilbert space, then the assignment $$\begin{aligned} (E,T)\mapsto T^*\circ P_{E^\bot } + P_{E}, \quad \text {where}\quad E\in \mathscr {G}(H)\quad \text {and}\quad T\in \mathcal {L}(E,E^\bot ), \end{aligned}$$ induces a real bi-analytic bijection from the total space of the tangent bundle, $$\mathbf {T}(\mathscr {G}(H))$$ , of $$\mathscr {G}(H)$$ onto $$\mathcal {I}(H)$$ (here, $$E^\bot $$ is the orthogonal complement of E, $$P_E\in \mathcal {L}(H)$$ is the orthogonal projection onto E, and $$T^*$$ is the adjoint of T). Notice that this real bi-analytic bijection is an affine map on each tangent plane. Furthermore, if for every $$E\in \mathscr {G}(H)$$ , we identify $$\mathcal {L}(E,E^\bot )$$ with a subspace of $$\mathcal {L}(H)$$ via the embedding $$S\mapsto S\circ P_E$$ , then the inclusion map from $$\mathbf {T}(\mathscr {G}(H))$$ to the trivial Banach bundle $$\mathscr {G}(H)\times \mathcal {L}(H)$$ is a real analytic immersion. Through this, we give a concrete idempotent in $$M_{n^2}\big (C(\mathscr {G}(\mathbb {K}^n))\big )$$ that represents the K-theory class of the tangent bundle $$\mathbf {T}(\mathscr {G}(\mathbb {K}^n))$$ , when $$\mathbb {K}$$ is either the real field or the complex field.

A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population.

Seed size and shape traits are important determinants of seed yield and appearance quality in soybean [Glycine max (L.) Merr.]. Understanding the genetic architecture of these traits is important to enable their genetic improvement through efficient and targeted selection in soybean breeding, and for the identification of underlying causal genes. To map seed size and shape traits in soybean, a recombinant inbred line (RIL) population developed from K099 (small seed size) × Fendou 16 (large seed size), was phenotyped in three growing seasons. A genetic map of the RIL population was developed using 1,485 genotyping by random amplicon sequencing-direct (GRAS-Di) and 177 SSR markers. Quantitative trait locus (QTL) mapping was conducted by inclusive composite interval mapping. As a result, 53 significant QTLs for seed size traits and 27 significant QTLs for seed shape traits were identified. Six of these QTLs (qSW8.1, qSW16.1, qSLW2.1, qSLT2.1, qSWT1.2, and qSWT4.3) were identified with LOD scores of 3.80–14.0 and R2 of 2.36%–39.49% in at least two growing seasons. Among the above significant QTLs, 24 QTLs were grouped into 11 QTL clusters, such as, three major QTLs (qSL2.3, qSLW2.1, and qSLT2.1) were clustered into a major QTL on Chr.02, named as qSS2. The effect of qSS2 was validated in a pair of near isogenic lines, and its candidate genes (Glyma.02G269400, Glyma.02G272100, Glyma.02G274900, Glyma.02G277200, and Glyma.02G277600) were mined. The results of this study will assist in the breeding programs aiming at improvement of seed size and shape traits in soybean.

Embedding of Besov Spaces and the Volterra Integral Operator

The boundedness and compactness of the inclusion mapping from Besov spaces to tent spaces are studied in this paper. Meanwhile, the boundedness, compactness, and essential norm of the Volterra integral operator T g from Besov spaces to a class of general function spaces are also investigated.

QTL mapping of seedling biomass and root traits under different nitrogen conditions in bread wheat (Triticum aestivum L.)

Plant nitrogen assimilation and use efficiency in the seedling's root system are beneficial for adult plants in field condition for yield enhancement. Identification of the genetic basis between root traits and N uptake plays a crucial role in wheat breeding. In the present study, 198 doubled haploid lines from the cross of Yangmai 16/Zhongmai 895 were used to identify quantitative trait loci (QTLs) underpinning four seedling biomass traits and five root system architecture (RSA) related traits. The plants were grown under hydroponic conditions with control, low and high N treatments (Ca(NO3)2·4H2O at 0, 0.05 and 2.0 mmol L−1, respectively). Significant variations among the treatments and genotypes, and positive correlations between seedling biomass and RSA traits (r=0.20 to 0.98) were observed. Inclusive composite interval mapping based on a high-density map from the Wheat 660K single nucleotide polymorphisms (SNP) array identified 51 QTLs from the three N treatments. Twelve new QTLs detected on chromosomes 1AL (1) in the control, 1DS (2) in high N treatment, 4BL (5) in low and high N treatments, and 7DS (3) and 7DL (1) in low N treatments, are first reported in influencing the root and biomass related traits for N uptake. The most stable QTLs (RRS.caas-4DS) on chromosome 4DS, which were related to ratio of root to shoot dry weight trait, was in close proximity of the Rht-D1 gene, and it showed high phenotypic effects, explaining 13.1% of the phenotypic variance. Twenty-eight QTLs were clustered in 12 genetic regions. SNP markers tightly linked to two important QTLs clusters C10 and C11 on chromosomes 6BL and 7BL were converted to kompetitive allele-specific PCR (KASP) assays that underpin important traits in root development, including root dry weight, root surface area and shoot dry weight. These QTLs, clusters and KASP assays can greatly improve the efficiency of selection for root traits in wheat breeding programmes.

Mapping CRISPR-Cas9 public and commercial innovation using The\xa0Lens institutional toolkit

CRISPR-Cas9 is a revolutionary technology because it is precise, fast and easy to implement, cheap and components are readily accessible. This versatility means that the technology can deliver a timely end product and can be used by many stakeholders. In plant cells, the technology can be applied to knockout genes by using CRISPR–Cas nucleases that can alter coding gene regions or regulatory elements, alter precisely a genome by base editing to delete or regulate gene expression, edit precisely a genome by homology-directed repair mechanism (cellular DNA), or regulate transcriptional machinery by using dead Cas proteins to recruit regulators to the promoter region of a gene. All these applications can be for: 1) Research use (Non commercial), 2) Uses related product components for the technology itself (reagents, equipment, toolkits, vectors etc), and 3) Uses related to the development and sale of derived end products based on this technology. In this contribution, we present a prototype report that can engage the community in open, inclusive and collaborative innovation mapping. Using the open data at the Lens.org platform and other relevant sources, we tracked, analyzed, organized, and assembled contextual and bridged patent and scholarly knowledge about CRISPR-Cas9 and with the assistance of a new Lens institutional capability, The Lens Report Builder, currently in beta release, mapped the public and commercial innovation pathways of the technology. When scaled, this capability will also enable coordinated editing and curation by credentialed experts to inform policy makers, businesses and private or public investment.

QTL mapping of root traits in wheat under different phosphorus levels using hydroponic culture

BackgroundPhosphorus (P) is an important in ensuring plant morphogenesis and grain quality, therefore an efficient root system is crucial for P-uptake. Identification of useful loci for root morphological and P uptake related traits at seedling stage is important for wheat breeding. The aims of this study were to evaluate phenotypic diversity of Yangmai 16/Zhongmai 895 derived doubled haploid (DH) population for root system architecture (RSA) and biomass related traits (BRT) in different P treatments at seedling stage using hydroponic culture, and to identify QTL using 660 K SNP array based high-density genetic map.ResultsAll traits showed significant variations among the DH lines with high heritabilities (0.76 to 0.91) and high correlations (r = 0.59 to 0.98) among all traits. Inclusive composite interval mapping (ICIM) identified 34 QTL with 4.64–20.41% of the phenotypic variances individually, and the log of odds (LOD) values ranging from 2.59 to 10.43. Seven QTL clusters (C1 to C7) were mapped on chromosomes 3DL, 4BS, 4DS, 6BL, 7AS, 7AL and 7BL, cluster C5 on chromosome 7AS (AX-109955164 - AX-109445593) with pleiotropic effect played key role in modulating root length (RL), root tips number (RTN) and root surface area (ROSA) under low P condition, with the favorable allele from Zhongmai 895.ConclusionsThis study carried out an imaging pipeline-based rapid phenotyping of RSA and BRT traits in hydroponic culture. It is an efficient approach for screening of large populations under different nutrient conditions. Four QTL on chromosomes 6BL (2) and 7AL (2) identified in low P treatment showed positive additive effects contributed by Zhongmai 895, indicating that Zhongmai 895 could be used as parent for P-deficient breeding. The most stable QTL QRRS.caas-4DS for ratio of root to shoot dry weight (RRS) harbored the stable genetic region with high phenotypic effect, and QTL clusters on 7A might be used for speedy selection of genotypes for P-uptake. SNPs closely linked to QTLs and clusters could be used to improve nutrient-use efficiency.

Mapping and validation of a major QTL for primary root length of soybean seedlings grown in hydroponic conditions

BackgroundThe root system provides nutrient absorption and is closely related to abiotic stress tolerance, but it is difficult to study the roots under field conditions. This study was conducted to identify quantitative trait loci (QTL) associated with primary root length (PRL) during soybean seedling growth in hydroponic conditions. A total of 103 F7 recombinant inbred lines (RILs) derived from a cross between K099 (short primary root) and Fendou 16 (long primary root) were used to identify QTL for PRL in soybean. The RIL population was genotyped with 223 simple sequence repeats markers covering 20 chromosomes. Phenotyping for primary root length was performed for 3-weeks plants grown in hydoponic conditions. The identified QTL was validated in near isogenic lines and in a separate RIL population.ResultsQTL analysis using inclusive composite interval mapping method identified a major QTL on Gm16 between SSR markers Sat_165 and Satt621, explaining 30.25 % of the total phenotypic variation. The identified QTL, qRL16.1, was further confirmed in a segregating population derived from a residual heterozygous line (RHLs-98). To validate qRL16.1 in a different genetic background, QTL analysis was performed in another F6 RIL population derived from a cross between Union (medium primary root) and Fendou 16, in which a major QTL was detected again in the same genomic region as qRL16.1, explaining 14 % of the total phenotypic variation for PRL. In addition, the effect of qRL16.1 was confirmed using two pair of near-isogenic lines (NILs). PRL was significantly higher in NILs possessing the qRL16.1 allele from Fendou 16 compared to allele from K099.ConclusionsThe qRL16.1 is a novel QTL for primary root length in soybean which provides important information on the genetic control of root development. Identification of this major QTL will facilitate positional cloning and DNA marker-assisted selection for root traits in soybean.