Assessment of genetic diversity and recombination in maize

Sequencing has revolutionized our approaches to understanding diversity and assessing biological questions. Multiple sequencing methods have been developed to catalog the genetic diversity of maize. The large size of the maize genome has made reduced representation sequencing an efficient approach to cataloging the diversity of maize. To assess diversity, tGBS, a reduced representation sequencing method, was developed to accurately genotype homozygous and heterozygous loci in a flexible manner in contrast to currently available methods. tGBS provides genotyping accuracies of \u3e 97% estimated from multiple maize populations, even at heterozygous loci. However, whole-genome sequencing and de novo genome assembly provide improved detection of certain forms of genetic variation, such as structural variation, at increased cost. Linked read sequencing, which incorporates long molecule information, has the potential to provide variant calls via efficient genome assembly. To test the use of linked read sequencing for structural variant discovery and reference genome assembly, de novo genome assembly with the linked read strategy was assessed in a maize inbred line. An assembly with ~120k contigs covering 50% of the genome was developed, and the assessed accuracy was determined to be high. Repeat content remains a challenge in maize linked read assembly, but appears to contain patterns that may be resolved using further computational developments. In addition to cataloging diversity, the process of recombination that generates and distributes variants must be understood. To better understand the distribution of recombination in genes which may generate new haplotypes or novel alleles, reduced representation sequencing was performed to identify thousands of crossovers and gene conversions. Intragenic recombination was shown to generate transgressive expression patterns. While intragenic crossovers localize to the 5’ ends of genes, gene conversions exhibit a random distribution. Furthermore, recombination is enriched in genomic regions with high levels of synteny, which may be a cause or a consequence of the maintenance of synteny

Worker personality: Another skill bias beyond education in the digital age

We present empirical evidence suggesting that technological progress in the digital age will be biased not only with respect to skills acquired through education but also with respect to noncognitive skills (personality). We measure the direction of technological change by estimated future digitalization probabilities of occupations, and noncognitive skills by the Big Five personality traits from several German worker surveys. Even though we control extensively for education and experience, we find that workers characterized by strong openness and emotional stability tend to be less susceptible to digitalization. Traditional indicators of human capital thus measure workers’ skill endowments only imperfectly

tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci

Conventional genotyping-by-sequencing (cGBS) strategies suffer from high rates of missing data and genotyping errors, particularly at heterozygous sites. tGBS® genotyping-by-sequencing is a novel method of genome reduction that employs two restriction enzymes to generate overhangs in opposite orientations to which (single-strand) oligos rather than (double-stranded) adaptors are ligated. This strategy ensures that only doubledigested fragments are amplified and sequenced. The use of oligos avoids the necessity of preparing adaptors and the problems associated with inter-adaptor annealing/ligation. Hence, the tGBS protocol simplifies the preparation of high-quality GBS sequencing libraries. During polymerase chain reaction (PCR) amplification, selective nucleotides included at the 3\u27-end of the PCR primers result in additional genome reduction as compared to cGBS. By adjusting the number of selective bases, different numbers of genomic sites are targeted for sequencing. Therefore, for equivalent amounts of sequencing, more reads per site are available for SNP calling. Hence, as compared to cGBS, tGBS delivers higher SNP calling accuracy (\u3e97–99%), even at heterozygous sites, less missing data per marker across a population of samples, and an enhanced ability to genotype rare alleles. tGBS is particularly well suited for genomic selection, which often requires the ability to genotype populations of individuals that are heterozygous at many loci

Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels

Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5\u27 ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed higher or lower levels of expression than did nonrecombinant alleles in any of ~100 RILs, implicating intragenic recombination in the generation of new variants upon which selection can act. Thousands of apparent gene conversion events were identified, allowing us to estimate the genome-wide rate of gene conversion at SNP sites (4.9 X 10-5). The density of syntenic genes (i.e., those conserved at the same genomic locations since the divergence of maize and sorghum) exhibits a substantial correlation with crossover frequency, whereas the density of nonsyntenic genes (i.e., those which have transposed or been lost subsequent to the divergence of maize and sorghum) shows little correlation, suggesting that crossovers occur at higher rates in syntenic genes than in nonsyntenic genes. Increased rates of crossovers in syntenic genes could be either a consequence of the evolutionary conservation of synteny or a biological process that helps to maintain synteny

Using Microsatellites to Understand the Physical Distribution of Recombination on Soybean Chromosomes

Soybean is a major crop that is an important source of oil and proteins. A number of genetic linkage maps have been developed in soybean. Specifically, hundreds of simple sequence repeat (SSR) markers have been developed and mapped. Recent sequencing of the soybean genome resulted in the generation of vast amounts of genetic information. The objectives of this investigation were to use SSR markers in developing a connection between genetic and physical maps and to determine the physical distribution of recombination on soybean chromosomes. A total of 2,188 SSRs were used for sequence-based physical localization on soybean chromosomes. Linkage information was used from different maps to create an integrated genetic map. Comparison of the integrated genetic linkage maps and sequence based physical maps revealed that the distal 25% of each chromosome was the most marker-dense, containing an average of 47.4% of the SSR markers and 50.2% of the genes. The proximal 25% of each chromosome contained only 7.4% of the markers and 6.7% of the genes. At the whole genome level, the marker density and gene density showed a high correlation (R2) of 0.64 and 0.83, respectively with the physical distance from the centromere. Recombination followed a similar pattern with comparisons indicating that recombination is high in telomeric regions, though the correlation between crossover frequency and distance from the centromeres is low (R2 = 0.21). Most of the centromeric regions were low in recombination. The crossover frequency for the entire soybean genome was 7.2%, with extremes much higher and lower than average. The number of recombination hotspots varied from 1 to 12 per chromosome. A high correlation of 0.83 between the distribution of SSR markers and genes suggested close association of SSRs with genes. The knowledge of distribution of recombination on chromosomes may be applied in characterizing and targeting genes

Linked read technology for assembling large complex and polyploid genomes

Background: Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for large, complex and polyploid genomes. The linked read strategy has the potential to enhance the value of short reads for genome assembly because all reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly. Results: Here we describe a de novo maize B73 genome assembly generated via linked read technology which contains ~ 172,000 scaffolds with an N50 of 89 kb that cover 50% of the genome. Based on comparisons to the B73 reference genome, 91% of linked read contigs are accurately assembled. Because it was possible to identify errors with \u3e 76% accuracy using machine learning, it may be possible to identify and potentially correct systematic errors. Complex polyploids represent one of the last grand challenges in genome assembly. Linked read technology was able to successfully resolve the two subgenomes of the recent allopolyploid, proso millet (Panicum miliaceum). Our assembly covers ~ 83% of the 1 Gb genome and consists of 30,819 scaffolds with an N50 of 912 kb. Conclusions: Our analysis provides a framework for future de novo genome assemblies using linked reads, and we suggest computational strategies that if implemented have the potential to further improve linked read assemblies, particularly for repetitive genomes

Assessment of genetic diversity and recombination in maize

Sequencing has revolutionized our approaches to understanding diversity and assessing biological questions. Multiple sequencing methods have been developed to catalog the genetic diversity of maize. The large size of the maize genome has made reduced representation sequencing an efficient approach to cataloging the diversity of maize. To assess diversity, tGBS, a reduced representation sequencing method, was developed to accurately genotype homozygous and heterozygous loci in a flexible manner in contrast to currently available methods. tGBS provides genotyping accuracies of > 97% estimated from multiple maize populations, even at heterozygous loci. However, whole-genome sequencing and de novo genome assembly provide improved detection of certain forms of genetic variation, such as structural variation, at increased cost. Linked read sequencing, which incorporates long molecule information, has the potential to provide variant calls via efficient genome assembly. To test the use of linked read sequencing for structural variant discovery and reference genome assembly, de novo genome assembly with the linked read strategy was assessed in a maize inbred line. An assembly with ~120k contigs covering 50% of the genome was developed, and the assessed accuracy was determined to be high. Repeat content remains a challenge in maize linked read assembly, but appears to contain patterns that may be resolved using further computational developments. In addition to cataloging diversity, the process of recombination that generates and distributes variants must be understood. To better understand the distribution of recombination in genes which may generate new haplotypes or novel alleles, reduced representation sequencing was performed to identify thousands of crossovers and gene conversions. Intragenic recombination was shown to generate transgressive expression patterns. While intragenic crossovers localize to the 5’ ends of genes, gene conversions exhibit a random distribution. Furthermore, recombination is enriched in genomic regions with high levels of synteny, which may be a cause or a consequence of the maintenance of synteny.</p

tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci

Conventional genotyping-by-sequencing (cGBS) strategies suffer from high rates of missing data and genotyping errors, particularly at heterozygous sites. tGBS® genotyping-by-sequencing is a novel method of genome reduction that employs two restriction enzymes to generate overhangs in opposite orientations to which (single-strand) oligos rather than (double-stranded) adaptors are ligated. This strategy ensures that only doubledigested fragments are amplified and sequenced. The use of oligos avoids the necessity of preparing adaptors and the problems associated with inter-adaptor annealing/ligation. Hence, the tGBS protocol simplifies the preparation of high-quality GBS sequencing libraries. During polymerase chain reaction (PCR) amplification, selective nucleotides included at the 3\u27-end of the PCR primers result in additional genome reduction as compared to cGBS. By adjusting the number of selective bases, different numbers of genomic sites are targeted for sequencing. Therefore, for equivalent amounts of sequencing, more reads per site are available for SNP calling. Hence, as compared to cGBS, tGBS delivers higher SNP calling accuracy (\u3e97–99%), even at heterozygous sites, less missing data per marker across a population of samples, and an enhanced ability to genotype rare alleles. tGBS is particularly well suited for genomic selection, which often requires the ability to genotype populations of individuals that are heterozygous at many loci