Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley.

BACKGROUND: Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage map construction, employing barley as a model system. Using the published high density EST-based SNP map in the Oregon Wolfe Barley (OWB) mapping population as a reference, we created a RAD map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both maps for detection of quantitative trait loci (QTL). RESULTS: Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines--the "dominant" and "recessive" marker stocks--and scored in a 93 member doubled haploid (DH) mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic map was constructed. The assembled RAD-only map consists of 445 markers with an average interval length of 5 cM, while an integrated map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total map lengths are comparable and the order of common markers is identical in both maps. The same large-effect QTL for reproductive fitness traits were detected with both maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley. CONCLUSIONS: We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic maps and association mapping.

Galphai generates multiple Pins activation states to link cortical polarity and spindle orientation in Drosophila neuroblasts.

Drosophila neuroblasts divide asymmetrically by aligning their mitotic spindle with cortical cell polarity to generate distinct sibling cell types. Neuroblasts asymmetrically localize Galphai, Pins, and Mud proteins; Pins/Galphai direct cortical polarity, whereas Mud is required for spindle orientation. It is currently unknown how Galphai-Pins-Mud binding is regulated to link cortical polarity with spindle orientation. Here, we show that Pins forms a "closed" state via intramolecular GoLoco-tetratricopeptide repeat (TPR) interactions, which regulate Mud binding. Biochemical, genetic, and live imaging experiments show that Galphai binds to the first of three Pins GoLoco motifs to recruit Pins to the apical cortex without "opening" Pins or recruiting Mud. However, Galphai and Mud bind cooperatively to the Pins GoLocos 2/3 and tetratricopeptide repeat domains, respectively, thereby restricting Pins-Mud interaction to the apical cortex and fixing spindle orientation. We conclude that Pins has multiple activity states that generate cortical polarity and link it with mitotic spindle orientation.

Protein domains govern the intracellular distribution of mouse sperm AKAP4.

A-kinase anchor proteins (AKAPs) spatially restrict cAMP-dependent protein kinase by tethering it to various cellular structures. In the polarized sperm cell, various compartmentalized functions, such as motility generated by the flagellum, are modulated by cAMP-dependent protein kinase. This important regulatory enzyme is associated with AKAP4, the principal component of the fibrous sheath; AKAP4 is synthesized as a precursor, pro-AKAP4, which is cleaved into mature AKAP4 during fibrous sheath assembly. To define the domains responsible for the intracellular distribution and assembly of AKAP4 into a macromolecular complex, various AKAP4-green fluorescent protein (GFP) constructs were introduced into somatic cell lines. The presence of the pro domain, either alone or as part of pro-AKAP4, resulted in a diffuse cytoplasmic localization of the GFP fusion protein, suggesting that, the pro domain keeps the AKAP4 precursor unassembled in vivo until it is transported to the developing tail structure and incorporated into the fibrous sheath. When the mature AKAP4-GFP fusion protein was expressed, it localized in a punctate cytoplasmic pattern. Two domains critical for this punctate localization, T2a and T2b, are homologous to the T2-tethering domain of rat AKAP5 that is important for binding to the actin cytoskeleton in transfected HEK293 cells. In contrast to AKAP5, the distribution of AKAP4 was dependent on the microtubular cytoskeleton. The interaction of AKAP4 with the microtubular network provides evidence that the longitudinal columns of the fibrous sheath, which contain AKAP4, may interact directly with the outer microtubular doublets of the sperm axoneme.

Differential RNA expression and polyribosome loading of alternative transcripts of the Akap4 gene in murine spermatids.

An X chromosome-linked gene, Akap4, is expressed only during spermiogenesis and encodes the major fibrous sheath protein of the mouse sperm flagellum. All sperm contain the AKAP4 protein even though only X chromosome-bearing spermatids express the gene, indicating that the Akap4 mRNA and/or protein must be shared among the conjoined spermatids via the intercellular bridges. There are two mouse Akap4 cDNA clones, Akap82 and Fsc1, which represent mRNAs that arise by alternative processing of a single gene. Although Akap82 and Fsc1 encode identical mature proteins, they differ in their 5' UTRs. We hypothesized that the expression pattern of these two mRNAs might be relevant to the issue of mRNA and/or protein transport into adjacent spermatids. Expression of both transcripts began in round spermatids, but the amount of the Akap82 transcript in condensing spermatids increased twofold relative to Fsc1. Significantly, only the Akap82 transcript was found on polyribosomes and translated in spermatids. These results indicate that the Akap82 transcript and/or its protein must be shared among the conjoined X and Y chromosome-bearing spermatids. Although Fsc1 was not polysomal, both the Akap82 and Fsc1 transcripts were deadenylated during spermiogenesis, suggesting that deadenylation is not always correlated with loading of mRNAs onto polyribosomes in germ cells. The distinct 5' UTR sequences in Akap82 and Fsc1 did not differ in their ability to regulate translation of reporter constructs either in vivo or in vitro. Antisense RNA transcripts complementary to both the Akap82 and Fsc1 mRNAs were present, suggesting that translatability may be regulated by these RNAs.