Set Of Recombinant Inbred Lines Research Articles

Identification of candidate genes for Fusarium head blight resistance from QTLs using RIL population in wheat.

Fusarium head blight (FHB) stands out as one of the most devastating wheat diseases and leads to significantly grain yield losses and quality reductions in epidemic years. Exploring quantitative trait loci (QTL) for FHB resistance is a critical step for developing new FHB-resistant varieties. We previously constructed a genetic map of unigenes (UG-Map) according to the physical positions using a set of recombinant-inbred lines (RILs) derived from the cross of 'TN18 × LM6' (TL-RILs). Here, the number of diseased spikelets (NDS) and relative disease index (RDI) for FHB resistance were investigated under four environments using TL-RILs, which were distributed across 13 chromosomes. A number of 36 candidate genes for NDS and RDI from of 19 stable QTLs were identified. The average number of candidate genes per QTL was 1.89, with 14 (73.7%), two (10.5%), and three (15.8%) QTLs including one, two, and 3-10 candidate genes, respectively. Among the 24 candidate genes annotated in the reference genome RefSeq v1.1, the homologous genes of seven candidate genes, including TraesCS4B02G227300 for QNds/Rdi-4BL-4553, TraesCS5B02G303200, TraesCS5B02G303300, TraesCS5B02G303700, TraesCS5B02G303800 and TraesCS5B02G304000 for QNds/Rdi-5BL-9509, and TraesCS7A02G568400 for QNds/Rdi-7AL-14499, were previously reported to be related to FHB resistance in wheat, barely or Brachypodium distachyon. These genes should be closely associated with FHB resistance in wheat. In addition, the homologous genes of five genes, including TraesCS1A02G037600LC for QNds-1AS-2225, TraesCS1D02G017800 and TraesCS1D02G017900 for QNds-1DS-527, TraesCS1D02G018000 for QRdi-1DS-575, and TraesCS4B02G227400 for QNds/Rdi-4BL-4553, were involved in plant defense responses against pathogens. These genes should be likely associated with FHB resistance in wheat.

Prezygotic mate selection is only partially correlated with the expression of NaS-like RNases and affects offspring phenotypes.

Nicotiana attenuata styles preferentially select pollen from among accessions with corresponding expression patterns of NaS-like-RNases (SLRs), and the postpollination ethylene burst (PPEB) is an accurate predictor of seed siring success. However, the ecological consequences of mate selection, its effect on the progeny, and the role of SLRs in the control of ethylene signaling remain unknown. We explored the link between the magnitude of the ethylene burst and expression of the SLRs in a set of recombinant inbred lines (RILs), dissected the genetic underpinnings of mate selection through genome-wide association study (GWAS), and examined its outcome for phenotypes in the next generation. We found that high levels of PPEB are associated with the absence of SLR2 in most of the tested RILs. We identified candidate genes potentially involved in the control of mate selection and showed that pollination of maternal genotypes with their favored pollen donors produces offspring with longer roots. When the maternal genotypes are only able to select against nonfavored pollen donors, the selection for such positive traits is abolished. We conclude that plants' ability of mate choice contributes to measurable changes in progeny phenotypes and is thus likely a target of selection.

Genome-wide association with transcriptomics reveals a shade-tolerance gene network in soybean

Shade tolerance is essential for soybeans in inter/relay cropping systems. A genome-wide association study (GWAS) integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance. An improved GWAS procedure, restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers (GASM-RTM-GWAS), identified 140 genes and their alleles associated with shade-tolerance index (STI), 146 with relative pith cell length (RCL), and nine with both. Annotation of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes, of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages. From the identified genes, three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network. Altogether, both STI and RCL gene systems worked for shade-tolerance with genes interacted each other, this confirmed that shade-tolerance is regulated by more than single group of interacted genes, involving multiple biological functions as a gene network.

Identification and fine mapping of qSW2 for leaf slow wilting in soybean

Drought is one of the abiotic stresses limiting the production of soybean (Glycine max). Elucidation of the genetic and molecular basis of the slow-wilting (SW) trait of this crop offers the prospect of its genetic improvement. A panel of 188 accessions and a set of recombinant inbred lines produced from a cross between cultivars Liaodou 14 and Liaodou 21 were used to identify quantitative-trait loci (QTL) associated with SW. Plants were genotyped by Specific-locus amplified fragment sequencing and seedling leaf wilting was assessed under three water-stress treatments. A genome-wide association study identified 26 SW-associated single-nucleotide polymorphisms (SNPs), including three located in a 248-kb linkage-disequilibrium (LD) block on chromosome 2. Linkage mapping revealed a major-effect QTL, qSW2, associated with all three treatments and adjacent to the LD block. Fine mapping in a BC2F3 population derived from a backcross between Liaodou 21 and R26 confined qSW2 to a 60-kb interval. Gene expression and sequence variation analysis identified the gene Glyma.02 g218100, encoding an auxin transcription factor, as a candidate gene for qSW2. Our results will contribute significantly to improving drought-resistant soybean cultivars by providing genetic information and resources.

Harnessing Deep Learning to Analyze Cryptic Morphological Variability ofMarchantia polymorpha.

Characterizing phenotypes is a fundamental aspect of biological sciences, although it can be challenging due to various factors. For instance, the liverwort Marchantia polymorpha is a model system for plant biology and exhibits morphological variability, making it difficult to identify and quantify distinct phenotypic features using objective measures. To address this issue, we utilized a deep-learning-based image classifier that can handle plant images directly without manual extraction of phenotypic features and analyzed pictures of M. polymorpha. This dioicous plant species exhibits morphological differences between male and female wild accessions at an early stage of gemmaling growth, although it remains elusive whether the differences are attributable to sex chromosomes. To isolate the effects of sex chromosomes from autosomal polymorphisms, we established a male and female set of recombinant inbred lines (RILs) from a set of male and female wild accessions. We then trained deep learning models to classify the sexes of the RILs and the wild accessions. Our results showed that the trained classifiers accurately classified male and female gemmalings of wild accessions in the first week of growth, confirming the intuition of researchers in a reproducible and objective manner. In contrast, the RILs were less distinguishable, indicating that the differences between the parental wild accessions arose from autosomal variations. Furthermore, we validated our trained models by an 'eXplainable AI' technique that highlights image regions relevant to the classification. Our findings demonstrate that the classifier-based approach provides a powerful tool for analyzing plant species that lack standardized phenotyping metrics.

Breeding safflower for adaptation to autumn sowing by interspecific hybridization

AbstractIn the light of current global climate change, gene introgression from wild relatives is a key strategy for increasing adaptation of crops that lost their variation during evolutionary bottleneck. Fall‐sown safflower leads to earlier spring growth and potentially higher productivity than the spring‐sown safflower, because of escaping from the terminal stresses of drought, heat, disease, and pests as well as efficient use of winter precipitation. During the last decade, we developed advanced generations of three sets of recombinant inbred lines (RILs) derived from three crosses of Carthamus tinctorius × Carthamus palaestinus (TP), C. tinctorius × Carthamus oxyacanthus (TO) and C. palaestinus × C. oxyacanthus (PO). The objectives of this study were to assess the efficiency of gene introgression from two wild relatives of safflower and genetic variation of derived RILs in terms of adaptation to autumn sowing and cold tolerance in the field. The results showed a continuous variation for seed yield and oil content in RILs, indicating the existence of transgressive segregation in lines. Comparison of three interspecific populations indicated that lines derived from TP crosses showed high potential for autumn planting, winter hardness, and productivity of seed and oil yield. However, the RILs derived from PO and TO had higher chlorophyll fluorescence (Fv/Fm) than TP population. Our results indicated that restoring lost genes in safflower is possible by introgression from its close relatives (especially C. palaestinus species). Identified superior RILs can be checked for other biotic and abiotic tolerance to develop new varieties in this valuable oil seed crop.

Mating success at elevated temperature is associated to thermal adaptation in a set of recombinant inbred lines of Drosophila melanogaster

In insects, mating ability at elevated temperature can be relevant for adaptation to heat-stressed environments and global warming. Here, we examined copulation latency (T1), copulation duration (T2), and mating frequency (T3, an index of mating success) in two related sets of recombinant inbred lines (RIL) in Drosophila melanogaster at both elevated (33 °C) and benign (25 °C) temperatures. One of these RIL sets (RIL-SH2) was shown to be consistently more resistant in both heat knockdown and heat-shock survival assays than its related set (RIL-D48) in previous studies. Negative correlations across RILs were found between T1 and T3 in this study. Flies from the heat-resistant set of RIL (RIL-SH2) were better able to mate at elevated temperature than flies from the heat-susceptible set (RIL-D48). Quantitative trait locus (QTL) mapping identified temperature-dependent QTLs for all traits (T1, T2 and T3) on all the three major chromosomes. Mating success at elevated temperature was found to be influenced by multiple QTLs. At elevated temperature, several QTLs for mating traits co-localized with QTLs that were previously associated with thermotolerance. The genetic basis for T1, T2 and T3 at the elevated temperature was found to be largely different from the genetic basis controlling the variation for mating success at benign temperature, as there was only a very low (or even null) number of QTLs overlapping across temperatures.

The Collaborative Cross Mouse – A Powerful Tool for Studying Complex Genetic Conditions of Neurogenesis and Brain Development

Neurodegenerative disorders (NDD), like Alzheimer’s disease (AD), impose a large health and socio-economic burden. AD affected 50 million people worldwide in 2019, and was the fifth leading cause of death for people over 65 years old. Despite the high prevalences of NDDs, very little is known about their underlying mechanisms and causes. Commonly occurring comorbidities and symptoms – such as cognitive impairment – overlap, complicating differential diagnosis. Recent studies have also noted large differences between the diagnostic outcomes associated with different genetic causes. In humans, multiple genetic variants are associated with neurogenesis and NDDs. Most research on NDDs uses animal models that focus on a single mutation in a fixed genetic background, providing inadequate heterogeneity and power to map genes linked to complex disease conditions. Therefore, it is imperative for NDD research to use next-generation animal models with greater genetic diversity. The Collaborative Cross (CC) mouse captures over 90% of the genetic diversity of the mouse species in a set of recombinant inbred lines to maximize genetic power. The CC model improves the outcomes of lab research: it enables population-based laboratory study, generates efficient and reproducible datasets, and allows researchers to identify multiple causative genetic factors for neurobehavioural traits. The convergence of all these characteristics will advance the translational value of laboratory research and create commercially viable, cost-effective clinical interventions.

The Collaborative Cross Mouse – A Powerful Tool for Studying Complex Genetic Conditions of Neurogenesis and Brain Development

Neurodegenerative disorders (NDD), like Alzheimer’s disease (AD), impose a large health and socio-economic burden. AD affected 50 million people worldwide in 2019, and was the fifth leading cause of death for people over 65 years old. Despite the high prevalences of NDDs, very little is known about their underlying mechanisms and causes. Commonly occurring comorbidities and symptoms – such as cognitive impairment – overlap, complicating differential diagnosis. Recent studies have also noted large differences between the diagnostic outcomes associated with different genetic causes. In humans, multiple genetic variants are associated with neurogenesis and NDDs. Most research on NDDs uses animal models that focus on a single mutation in a fixed genetic background, providing inadequate heterogeneity and power to map genes linked to complex disease conditions. Therefore, it is imperative for NDD research to use next-generation animal models with greater genetic diversity. The Collaborative Cross (CC) mouse captures over 90% of the genetic diversity of the mouse species in a set of recombinant inbred lines to maximize genetic power. The CC model improves the outcomes of lab research: it enables population-based laboratory study, generates efficient and reproducible datasets, and allows researchers to identify multiple causative genetic factors for neurobehavioural traits. The convergence of all these characteristics will advance the translational value of laboratory research and create commercially viable, cost-effective clinical interventions.

Validation of molecular markers linked to flowering time genes in chickpea (Cicer arietinum L.)

The objective of the study was to validate molecular markers linked to genomic regions controlling flowering time in a set of Recombinant Inbred Lines (RILs) population derived from Pusa 362 (Late) x BGD 132 (Early) and 21 diverse genotypes differing in time of flowering in chickpea (Cicer arietinum L.). The study of the polymorphic survey between parents using 27 linked markers of chickpea and Arabidopsis found 8 of them polymorphic. Bulked Segregant Analysis identified TA64 and TA142 as putatively linked to efl3 locus governing early flowering in chickpea that can be utilized for marker assisted selection. The PCR amplification of 6 polymorphic markers in germplasm showed the presence of one or more alleles in many of them (up to 3), indicating the complex nature of flowering time in chickpea. The amplification pattern of CaEfl3a-F1 marker linked to Efl3 early flowering allele of Arabidopsis in 21 chickpea germplasm indicated the presence of some conserved genomic sequences controlling flowering time in the two species.

Genetic architecture of variation in Arabidopsis thaliana rosettes.

Rosette morphology across Arabidopsis accessions exhibits considerable variation. Here we report a high-throughput phenotyping approach based on automatic image analysis to quantify rosette shape and dissect the underlying genetic architecture. Shape measurements of the rosettes in a core set of Recombinant Inbred Lines from an advanced mapping population (Multiparent Advanced Generation Inter-Cross or MAGIC) derived from inter-crossing 19 natural accessions. Image acquisition and analysis was scaled to extract geometric descriptors from time stamped images of growing rosettes. Shape analyses revealed heritable morphological variation at early juvenile stages and QTL mapping resulted in over 116 chromosomal regions associated with trait variation within the population. Many QTL linked to variation in shape were located near genes related to hormonal signalling and signal transduction pathways while others are involved in shade avoidance and transition to flowering. Our results suggest rosette shape arises from modular integration of sub-organ morphologies and can be considered a functional trait subjected to selective pressures of subsequent morphological traits. On an applied aspect, QTLs found will be candidates for further research on plant architecture.

Major Genomic Regions for Wheat Grain Weight as Revealed by QTL Linkage Mapping and Meta-Analysis.

Grain weight is a key determinant for grain yield potential in wheat, which is highly governed by a type of quantitative genetic basis. The identification of major quantitative trait locus (QTL) and functional genes are urgently required for molecular improvements in wheat grain yield. In this study, major genomic regions and putative candidate genes for thousand grain weight (TGW) were revealed by integrative approaches with QTL linkage mapping, meta-analysis and transcriptome evaluation. Forty-five TGW QTLs were detected using a set of recombinant inbred lines, explaining 1.76-12.87% of the phenotypic variation. Of these, ten stable QTLs were identified across more than four environments. Meta-QTL (MQTL) analysis were performed on 394 initial TGW QTLs available from previous studies and the present study, where 274 loci were finally refined into 67 MQTLs. The average confidence interval of these MQTLs was 3.73-fold less than that of initial QTLs. A total of 134 putative candidate genes were mined within MQTL regions by combined analysis of transcriptomic and omics data. Some key putative candidate genes similar to those reported early for grain development and grain weight formation were further discussed. This finding will provide a better understanding of the genetic determinants of TGW and will be useful for marker-assisted selection of high yield in wheat breeding.

Genetics of fertility restoration in A1 Cytoplasmic Genetic Male Sterility (CGMS) systems in Sorghum (Sorghum bicolor L. Moench)

The cause of Cytoplasmic Genetic Male Sterility (CGMS) is specific nuclear and mitochondrial interactions. Almost all commercial sorghum hybrids were developed using the A1 cytoplasmic genetic male sterility system. Understanding the inheritance of fertility restoration in sorghum for A1 cytoplasm, for example, can improve the selection efficiency of restorer lines for increased seed production. In a cross of male sterile line 296A with A1 cytoplasm and restorer lines comprised of a set of Recombinant Inbred Lines (RILs), the inheritance pattern of fertility restoration of sorghum was studied. The F1 hybrid was completely fertile, revealing the dominant nature of fertility restoration, which is controlled by one or two major genes with modifiers. In this study, the genetics of fertility restoration of the A1 cytoplasmic nuclear male sterility system (CGMS) in sorghum were investigated in segregating F2 and BC1 populations of A1 cytoplasm crosses. Fertility restoration was governed by a monogenic inheritance (3F:1S) mechanism represented by a single dominant gene responsible for fertility restoration in all of the crosses studied.

Genetic variation in the heat-stress survival of embryos is largely decoupled from adult thermotolerance in an intercontinental set of recombinant lines of Drosophila melanogaster.

In insects, thermal adaptation works on the genetic variation for thermotolerance of not only larvae and adults but also of the immobile stages of the life cycle including eggs. In contrast to adults and larvae, the genetic basis for thermal adaptation in embryos (eggs) remains to be tested in the model insect Drosophila melanogaster. Quantitative-trait loci (QTL) for heat-stress resistance in embryos could largely differ from previously identified QTL for larvae and adults. Here we used an intercontinental set of recombinant inbred lines (RIL), which were previously used to identify thermotolerance-QTLs in adults and larvae because of their high variation segregating for adult thermotolerance. Eggs appeared to be more heat resistant than larvae and adults from previous studies on these RIL, though different heat-shock assays were used in previous studies. We found that variation in thermotolerance in embryos can be, at least partially, genetically decoupled from thermotolerance in the adult insect. Some RIL that are heat resistant in the adult and larvae can be heat susceptible in embryos. Only one small-effect QTL out of five autosomal QTL co-localized between embryo and other ontogenetic stages. These results suggest that selection for thermal adaptation in adult flies and larvae is predicted to have only a small impact on embryo thermotolerance. In addition, heat-stress tolerance of insects can be measured across ontogenetic stages including embryos in order to better predict thermal adaptive limits of populations and species.

Evaluation of Seed Dormancy, One of the Key Domestication Traits in Chickpea

Legume seed dormancy has been altered during the domestication process, resulting in non-dormant seeds with a testa that is readily permeable for water. Ultimately, this provides fast and uniform germination, in contrast to dormant seeds of the wild progenitor. To date, germination and seed dormancy were studied mostly in relation to two types of cultivated chickpea: kabuli and desi. We studied seed dormancy, from physiological and anatomical perspectives, in chickpea crops and compared cultivated chickpeas to the wild chickpea progenitor and set of recombinant inbred lines (RIL). There was significant difference in the macrosclereid length of parental genotypes. Cultivated chickpea (C. arietinum, ICC4958) had mean of 125 µm, while wild C. reticulatum (PI48977) had a mean of 165 µm. Histochemical staining of the seed coat also showed differences, mainly in terms of Sudan Red detection of lipidic substances. Imbibition and germination were tested and several germination coefficients were calculated. Cultivated chickpea seeds imbibed readily within 24 h, while the germination percentage of wild chickpea at various times was 36% (24 h), 46% (48 h), 60% (72 h) and reached 100% only after 20 days. RIL lines showed a broader distribution. This knowledge will ultimately lead to the identification of the underlying molecular mechanism of seed dormancy in chickpea, as well as allowing comparison to phylogenetically related legumes, such as pea, lentil and faba bean, and could be utilized in chickpea breeding programs.

Relationships between Stalk Resistance and Corn Borers, Agronomic Traits, and Cell Wall Hydroxycinnamates in a Set of Recombinant Inbred Lines from a Maize MAGIC Population

Corn borers are the most important pest affecting maize. Resistance to corn borer attack may compromise plant fitness being detrimental for some important agronomic traits such as yield. Against the attack of this pest, cell wall-bound hydroxycinnamates have been previously described as a possible defense mechanism. In this study, agronomic characterization and cell wall-bound hydroxycinnamates quantification was performed in a subset of Recombinant Inbred Lines (RILs) from a Multiparent Advanced Generation Intercross (MAGIC) population that showed contrasting behavior against corn borer attack. Resistant lines showed greater concentration of p-coumaric acid, the only hydroxycinnamate that could have a role in the resistance in these particular materials. In addition, results indicated that resistant lines showed precocity, low grain moisture at harvest, and reduced plant height, thus, selecting for resistance may be detrimental for yield. In this way, a breeding strategy directly targeting grain yield in order to tolerate corn borer attack would be the recommended one.

Detecting QTL system of root hydraulic stress tolerance index at seedling stage in soybean

<p indent=0mm>Soybean is an important source of plant protein and vegetable oil in the world. Drought is one of the important environmental stress factors affecting soybean yield. To explore the genetic base of drought tolerance in soybean, a nested association mapping population composed of two sets of recombinant inbred lines with a common parent in a total of 429 lines was investigated for leaf proline content under PEG simulated drought stress. The genetic system of root hydraulic stress tolerance index (RHSTI) was analyzed using the RTM-GWAS (restrictive two-stage multilocus genome-wide association study). The results showed that there were significant differences in RHSTI among the three parents under two different environments in spring and summer, and among the nested association mapping population with the variation range of 0.11–2.94 and 0.03–1.93, respectively. The heritability values of Line and Line×Environment were 37.9% and 60.1%, respectively, indicating that the variation of RHSTI was greatly affected by the environment. Using the RHSTI data and 6137 SNPLDB markers, a total of 45 main effect QTLs were detected on 18 chromosomes, which could explain a total of 37.58% phenotypic variation, including 7 large contribution QTLs with <italic>R</italic>² more than 1%. Among them, 34 QTLs with QTL×Environment effect explained 12.50% of the phenotypic variation. Combined with the transcriptome data under PEG stress, totally 38 differentially expressed genes were identified within a QTL ± 500 kb, which can be grouped into different biological categories, including ABA responders, stress responders, transcription factors, development factors, protein metabolism factors, unknown functions and others, with stress responses, transcription factors and development factors as the major parts. In summary, the results indicated that the drought tolerance of soybean was a complex quantitative trait, with the complex genetic basis controlling by multiple loci, multiple genes and interaction with the environment. The present results can lay the foundation of molecular breeding for drought tolerance in soybean.

Carbohydrate Accumulation and Differential Transcript Expression in Winter Wheat Lines with Different Levels of Snow Mold and Freezing Tolerance after Cold Treatment.

Winter wheat (Triticum aestivum L.) undergoes a period of cold acclimation in order to survive the ensuing winter, which can bring freezing temperatures and snow mold infection. Tolerance of these stresses is conferred in part by accumulation of carbohydrates in the crown region. This study investigates the contributions of carbohydrate accumulation during a cold treatment among wheat lines that differ in their snow mold tolerance (SMT) or susceptibility (SMS) and freezing tolerance (FrT) or susceptibility (FrS). Two parent varieties and eight recombinant inbred lines (RILs) were analyzed. The selected RILs represent four combinations of tolerance: SMT/FrT, SMT/FrS, SMS/FrT, and SMS/FrS. It is hypothesized that carbohydrate accumulation and transcript expression will differ between sets of RILs. Liquid chromatography with a refractive index detector was used to quantify carbohydrate content at eight time points over the cold treatment period. Polysaccharide and sucrose content differed between SMT and SMS RILs at various time points, although there were no significant differences in glucose or fructose content. Glucose and fructose content differed between FrT and FrS RILs in this study, but no significant differences in polysaccharide or sucrose content. RNAseq was used to investigate differential transcript expression, followed by modular enrichment analysis, to reveal potential candidates for other mechanisms of tolerance, which included expected pathways such as oxidative stress, chitinase activity, and unexpected transcriptional pathways. These differences in carbohydrate accumulation and differential transcript expression begin to give insight into the differences of wheat lines when exposed to cold temperatures.

Detection of QTL for phosphorus efficiency and biomass traits at the seedling stage in wheat

Phosphorus (P) is one of the most vital nutrient elements in crop output and quality formation. In this study, four biomass, four P uptake efficiency (PupE), and three P-utilization efficiency (PutE) traits were investigated using a set of recombinant inbred lines (RILs) derived from a cross of “SN0431 × LM21”, under hydroponic culture trials at low P (LP) and normal P (NP) levels in two different seasons, respectively. A total of 85 QTL were identified on 18 chromosomes except for 1D, 2A, and 3D. Among them, 36 and 42 QTL were detected under LP and NP, respectively, and seven QTL were simultaneously detected under LP and NP. Seventeen relatively high-frequency QTL (RHF-QTL) were detected. The average contributions of 13 major RHF-QTL were over 10.00%. Five important QTL clusters were detected on chromosomes 4D, 5A, and 5B. Among them, positive linkages were observed between PutE and biomass traits at four QTL clusters, C1, C2, C3, and C6, showing these loci may be hot spots for genetic control of both phosphorus utilization and biomass accumulation in wheat seedlings. In addition, correlation analysis indicated that three biomass traits (SDW, RDW, and TDW) should be used as primary selection indexes for PE at the seedling stage.

The Dawn of the Age of Multi-Parent MAGIC Populations in Plant Breeding: Novel Powerful Next-Generation Resources for Genetic Analysis and Selection of Recombinant Elite Material.

The compelling need to increase global agricultural production requires new breeding approaches that facilitate exploiting the diversity available in the plant genetic resources. Multi-parent advanced generation inter-cross (MAGIC) populations are large sets of recombinant inbred lines (RILs) that are a genetic mosaic of multiple founder parents. MAGIC populations display emerging features over experimental bi-parental and germplasm populations in combining significant levels of genetic recombination, a lack of genetic structure, and high genetic and phenotypic diversity. The development of MAGIC populations can be performed using “funnel” or “diallel” cross-designs, which are of great relevance choosing appropriate parents and defining optimal population sizes. Significant advances in specific software development are facilitating the genetic analysis of the complex genetic constitutions of MAGIC populations. Despite the complexity and the resources required in their development, due to their potential and interest for breeding, the number of MAGIC populations available and under development is continuously growing, with 45 MAGIC populations in different crops being reported here. Though cereals are by far the crop group where more MAGIC populations have been developed, MAGIC populations have also started to become available in other crop groups. The results obtained so far demonstrate that MAGIC populations are a very powerful tool for the dissection of complex traits, as well as a resource for the selection of recombinant elite breeding material and cultivars. In addition, some new MAGIC approaches that can make significant contributions to breeding, such as the development of inter-specific MAGIC populations, the development of MAGIC-like populations in crops where pure lines are not available, and the establishment of strategies for the straightforward incorporation of MAGIC materials in breeding pipelines, have barely been explored. The evidence that is already available indicates that MAGIC populations will play a major role in the coming years in allowing for impressive gains in plant breeding for developing new generations of dramatically improved cultivars.