Extensive genomic characterization of a set of near-isogenic lines for heterotic QTL in maize (Zea mays L.)

Background Despite the crucial role that heterosis has played in crop improvement, its genetic and molecular bases are still elusive. Several types of structured populations were used to discover the genetic architecture underlying complex phenotypes, and several QTL related to heterosis were detected. However, such analyses generally lacked the statistical power required for the detailed characterization of individual QTL. Currently, QTL introgression into near-isogenic materials is considered the most effective strategy to this end, despite such materials inevitably contain a variable, unknown and undesired proportion of non-isogenic genome. An introgression program based on residual heterozygous lines allowed us to develop five pairs of maize (Zea mays L.) near-isogenic lines (NILs) suitable for the fine characterization of three major heterotic QTL previously detected. Here we describe the results of the detailed genomic characterization of these NILs that we undertook to establish their genotypic structure, to verify the presence of the expected genotypes within target QTL regions, and to determine the extent and location of residual non-isogenic genomic regions. Results The SNP genotyping approach allowed us to determine the parent-of-origin allele for 14,937 polymorphic SNPs and to describe in detail the genotypic structure of all NILs. The correct introgression was confirmed for all target QTL in the respective NIL and several nonisogenic regions were detected genome-wide. Possible linkage drag effects associated to the specific introgressed regions were observed. The extent and position of other non-isogenic regions varied among NIL pairs, probably deriving from random segregating sections still present at the separation of lineages within pairs. Conclusions The results of this work strongly suggest that the actual isogenicity and the genotypic architecture of near-isogenic materials should be monitored both during the introgression procedure and on the final materials as a paramount requisite for a successful mendelization of target QTL. The information here gathered on the genotypic structure of NILs will be integrated in future experimental programs aimed at the fine mapping and isolation of major heterotic QTL, a crucial step towards the understanding of the molecular bases of heterosis in maize

QTL controlling root and shoot traits of maize seedlings under cold stress

The improvement of early vigour is crucial for the adaptation of maize (Zea mays L.) to the climatic conditions of central Europe and the northern Mediterranean, where early sowing is an important strategy for avoiding the effect of summer drought. The objectives of this study were to identify quantitative trait loci (QTL) controlling cold-related traits and to investigate the relationships among them. A set of 168 F2:4 families of the Lo964×Lo1016 cross was grown in a sand-vermiculite substrate at 15/13°C (day/night) until the one-leaf stage. Twenty QTL were identified for the four shoot and two seed traits examined. Analysis of root weight and digital measurements of the length and diameter of primary and seminal roots led to the identification of 40 QTL. The operating efficiency of photosystemII (ΦPSII) was related to seedling dry weight at both the phenotypic and genetic level (r=0.46, two matching loci, respectively) but was not related to root traits. Cluster analysis and QTL association revealed that the different root traits were largely independently inherited and that root lengths and diameters were mostly negatively correlated. The major QTL for root traits detected in an earlier study in hydroponics were confirmed in this study. The length of the primary lateral roots was negatively associated with the germination index (r=−0.38, two matching loci). Therefore, we found a large number of independently inherited loci suitable for the improvement of early seedling growth through better seed vigour and/or a higher rate of photosynthesi

High-density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding

Durum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, and yet, its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here, we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81 587 markers scoring 30 155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome-specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years and use this information to conduct a genome-wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker-assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analysed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat

Genome wide association study to identify the genetic base of smallholder farmer preferences of Durum wheat traits

Smallholder agriculture involves millions of farmers worldwide. A methodical utilization of their traditional knowledge in modern breeding efforts may help the production of locally adapted varieties better addressing their needs. In this study, a combination of participatory approaches, genomics, and quantitative genetics is used to trace the genetic basis of smallholder farmer preferences of durum wheat traits. Two smallholder communities evaluated 400 Ethiopian wheat varieties, mostly landraces, for traits of local interest in two locations in the Ethiopian highlands. For each wheat variety, farmers provided quantitative evaluations of their preference for flowering time, spike morphology, tillering capacity, and overall quality. Ten agronomic and phenology traits were simultaneously measured on the same varieties, providing the means to compare them with farmer traits. The analysis of farmer traits showed that they were partially influenced by gender and location but were repeatable and heritable, in some cases more than metric traits. The durum wheat varieties were genotyped for more than 80,000 SNP markers, and the resulting data was used in a genome wide association (GWA) study providing the molecular dissection of smallholder farmers' choice criteria

Dissecting the effect of heat stress on durum wheat under field conditions

Introduction: Heat stress negatively affects wheat production in several ways, mainly by reducing growth rate, photosynthetic capacity and reducing spike fertility. Modeling stress response means analyzing simultaneous relationships among traits affecting the whole plant response and determinants of grain yield. The aim of this study was to dissect the diverse impacts of heat stress on key yield traits and to identify the most promising sources of alleles for heat tolerance. Methods: We evaluated a diverse durum wheat panel of 183 cultivars and breeding lines from worldwide, for their response to long-term heat stress under field conditions (HS) with respect to non stress conditions (NS), considering phenological traits, grain yield (GY) and its components as a function of the timing of heat stress and climatic covariates. We investigated the relationships among plant and environmental variables by means of a structural equation model (SEM) and Genetic SEM (GSEM). Results: Over two years of experiments at CENEB, CIMMYT, the effects of HS were particularly pronounced for the normalized difference vegetation index, NDVI (-51.3%), kernel weight per spike, KWS (-40.5%), grain filling period, GFP (-38.7%), and GY (-56.6%). Average temperatures around anthesis were negatively correlated with GY, thousand kernel weight TKW and test weight TWT, but also with spike density, a trait determined before heading/anthesis. Under HS, the correlation between the three major determinants of GY, i.e., fertile spike density, spike fertility and kernel size, were of noticeable magnitude. NDVI measured at medium milk-soft dough stage under HS was correlated with both spike fertility and grain weight while under NS it was less predictive of grain weight but still highly correlated with spike fertility. GSEM modeling suggested that the causal model of performance under HS directly involves genetic effects on GY, NDVI, KWS and HD. Discussion: We identified consistently suitable sources of genetic resistance to heat stress to be used in different durum wheat pre-breeding programs. Among those, Desert Durums and CIMMYT’80 germplasm showed the highest degree of adaptation and capacity to yield under high temperatures and can be considered as a valuable source of alleles for adaptation to breed new HS resilient cultivars

Exceptional Driving Principles for Autonomous Vehicles

Public expectations for automated vehicles span a broad range, from mobility for passengers, to road user safety, to compliance with the traffic code. In most ordinary situations, these expectations can be satisfied simultaneously. But these various expectations can also lead to exceptional scenarios where certain objectives, such as those related to safety, are in tension with road rules. Exceptional driving scenarios challenge motion planning algorithms in automated vehicles to find solutions that are legally grounded, ethically sound, and technically feasible. The general public’s familiarity with exceptional driving scenarios comes from the classic Trolley Car problem in philosophy, asking who should live and who should die in an unavoidable collision. These discussions tend to take a consequentialist view by framing the ethical action as the one that achieves the best outcome. By taking a different perspective that views driving as a social contract, the AV\u27s ethical obligations are limited to meeting the duty of care owed to other road users. With this perspective, the existing legal system in the US provides a framework for choosing appropriate behaviors in exceptional driving cases and for answering the Trolley Car problem. This work outlines principles that prioritize care for humans, respect the authority of human-defined traffic law, and ensure that the vehicle avoids decisions that introduce unreasonable risks. Developing AVs that can legally and ethically negotiate exceptional driving scenarios is simply a matter of translating the principles into engineering requirements with no need for new laws or endless philosophical debate

Alternative patterns of sex chromosome differentiation in Aedes aegypti (L).

BACKGROUND: Some populations of West African Aedes aegypti, the dengue and zika vector, are reproductively incompatible; our earlier study showed that divergence and rearrangements of genes on chromosome 1, which bears the sex locus (M), may be involved. We also previously described a proposed cryptic subspecies SenAae (PK10, Senegal) that had many more high inter-sex FST genes on chromosome 1 than did Ae.aegypti aegypti (Aaa, Pai Lom, Thailand). The current work more thoroughly explores the significance of those findings. RESULTS: Intersex standardized variance (FST) of single nucleotide polymorphisms (SNPs) was characterized from genomic exome capture libraries of both sexes in representative natural populations of Aaa and SenAae. Our goal was to identify SNPs that varied in frequency between males and females, and most were expected to occur on chromosome 1. Use of the assembled AaegL4 reference alleviated the previous problem of unmapped genes. Because the M locus gene nix was not captured and not present in AaegL4, the male-determining locus, per se, was not explored. Sex-associated genes were those with FST values ≥ 0.100 and/or with increased expected heterozygosity (H exp , one-sided T-test, p < 0.05) in males. There were 85 genes common to both collections with high inter-sex FST values; all genes but one were located on chromosome 1. Aaa showed the expected cluster of high inter-sex FST genes proximal to the M locus, whereas SenAae had inter-sex FST genes along the length of chromosome 1. In addition, the Aaa M-locus proximal region showed increased H exp levels in males, whereas SenAae did not. In SenAae, chromosomal rearrangements and subsequent suppressed recombination may have accelerated X-Y differentiation. CONCLUSIONS: The evidence presented here is consistent with differential evolution of proto-Y chromosomes in Aaa and SenAae

Root system architecture in Italian maize inbred lines: toward applications in breeding programs

Identifying genotypes with efficient Root System Architecture (RSA) and resilient to drought and heat stresses could mitigate the negative effects of climate change and contribute to adapt to new hostile environments. Preliminary investigations showed a vast genetic and phenotypic variability in root traits among elite cultivars and germplasm populations that could be used as source of useful alleles for stress tolerance. The goal of this study is to define phenotypic and genomic selection criteria to discover drought tolerant root ideotypes through a deep evaluation of root traits