Novel strategies for genomic prediction of untested single-cross maize hybrids using unbalanced historical data.

KEY MESSAGE: Weighted outperformed unweighted genomic prediction using an unbalanced dataset representative of a commercial breeding program. Moreover, the use of the two cycles preceding predictions as training set achieved optimal prediction ability. Predicting the performance of untested single-cross hybrids through genomic prediction (GP) is highly desirable to increase genetic gain. Here, we evaluate the predictive ability (PA) of novel genomic strategies to predict single-cross maize hybrids using an unbalanced historical dataset of a tropical breeding program. Field data comprised 949 single-cross hybrids evaluated from 2006 to 2013, representing eight breeding cycles. Hybrid genotypes were inferred based on their parents' genotypes (inbred lines) using single-nucleotide polymorphism markers obtained via genotyping-by-sequencing. GP analyses were fitted using genomic best linear unbiased prediction via a stage-wise approach, considering two distinct cross-validation schemes. Results highlight the importance of taking into account the uncertainty regarding the adjusted means at each step of a stage-wise analysis, due to the highly unbalanced data structure and the expected heterogeneity of variances across years and locations of a commercial breeding program. Further, an increase in the size of the training set was not always advantageous even in the same breeding program. The use of the two cycles preceding predictions achieved optimal PA of untested single-cross hybrids in a forward prediction scenario, which could be used to replace the first step of field screening. Finally, in addition to the practical and theoretical results applied to maize hybrid breeding programs, the stage-wise analysis performed in this study may be applied to any crop historical unbalanced data.

DNA polymorphisms as tools for spinal cord injury research.

STUDY DESIGN: Data mining of single nucleotide polymorphisms (SNPs) in gene pathways related to spinal cord injury (SCI). OBJECTIVES: To identify gene polymorphisms putatively implicated with neuronal damage evolution pathways, potentially useful to SCI study. SETTING: Departments of Psychiatry and Orthopedics, Faculdade de Medicina, Universidade de São Paulo, Brazil. METHODS: Genes involved with processes related to SCI, such as apoptosis, inflammatory response, axonogenesis, peripheral nervous system development and axon ensheathment, were determined by evaluating the 'Biological Process' annotation of Gene Ontology (GO). Each gene of these pathways was mapped using MapViewer, and gene coordinates were used to identify their polymorphisms in the SNP database. As a proof of concept, the frequency of subset of SNPs, located in four genes (ALOX12, APOE, BDNF and NINJ1) was evaluated in the DNA of a group of 28 SCI patients and 38 individuals with no SC lesions. RESULTS: We could identify a total of 95,276 SNPs in a set of 588 genes associated with the selected GO terms, including 3912 nucleotide alterations located in coding regions of genes. The five non-synonymous SNPs genotyped in our small group of patients, showed a significant frequency, reinforcing their potential use for the investigation of SCI evolution. CONCLUSION: Despite the importance of SNPs in many aspects of gene expression and protein activity, these gene alterations have not been explored in SCI research. Here we describe a set of potentially useful SNPs, some of which could underlie the genetic mechanisms involved in the post trauma spinal cord damage.

WITHDRAWN: Association between polymorphisms in genes of inflammatory response and axonal repair with spinal cord injury.

Ahead of Print article withdrawn by publisher. Please see re-submitted article 'DNA polymorphisms as tools for spinal cord injury research' Spinal Cord advance online publication, 20 May 2008; doi:10.1038/sc.2008.67.

Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade.

The mtDNA haplogroup L3e, which is identified by the restriction site +2349 MboI within the Afro-Eurasian superhaplogroup L3 (-3592 HpaI), is omnipresent in Africa but virtually absent in Eurasia (except for neighbouring areas with limited genetic exchange). L3e was hitherto poorly characterised in terms of HVS-I motifs, as the ancestral HVS-I type of L3e cannot be distinguished from the putative HVS-I ancestor of the entire L3 (differing from the CRS by a transition at np 16223). An MboI screening at np 2349 of a large number of Brazilian and Caribbean mtDNAs (encompassing numerous mtDNAs of African ancestry), now reveals that L3e is subdivided into four principal clades, each characterised by a single mutation in HVS-I, with additional support coming from HVS-II and partial RFLP analysis. The apparently oldest of these clades (transition at np 16327) occurs mainly in central Africa and was probably carried to southern Africa with the Bantu expansion(s). The most frequent clade (transition at np 16320) testifies to a pronounced expansion event in the mid-Holocene and seems to be prominent in many Bantu groups from all of Africa. In contrast, one clade (transition at np 16264) is essentially restricted to Atlantic western Africa (including Cabo Verde). We propose a tentative L3e phylogeny that is based on 197 HVS-I sequences. We conclude that haplogroup L3e originated in central or eastern Africa about 46,000 (+/-14,000) years ago, and was a hitchhiker of much later dispersal and local expansion events, with the rise of food production and iron smelting. Enforced migration of African slaves to the Americas translocated L3e mitochondria, the descendants of which in Brazil and the Caribbean still reflect their different regional African ancestries.

The ancestry of Brazilian mtDNA lineages.

We have analyzed 247 Brazilian mtDNAs for hypervariable segment (HVS)-I and selected restriction fragment-length-polymorphism sites, to assess their ancestry in different continents. The total sample showed nearly equal amounts of Native American, African, and European matrilineal genetic contribution but with regional differences within Brazil. The mtDNA pool of present-day Brazilians clearly reflects the imprints of the early Portuguese colonization process (involving directional mating), as well as the recent immigrant waves (from Europe) of the last century. The subset of 99 mtDNAs from the southeastern region encompasses nearly all mtDNA haplogroups observed in the total Brazilian sample; for this regional subset, HVS-II was analyzed, providing, in particular, some novel details of the African mtDNA phylogeny.

Molecular cloning of cDNAs encoding insecticidal neurotoxic peptides from the spider Phoneutria nigriventer.

From a Phoneutria nigriventer venom gland cDNA library several clones coding for the insect specific neurotoxin Tx4(6-1) were isolated. cDNA analysis showed that the encoded protein contained three distinct segments, comprising a signal sequence of 16 amino acids, followed by a glutamate-rich sequence of 18 amino acids and, finally, the coding region for the mature toxin. The deduced amino acid sequence for the mature polypeptide was identical to the protein sequence determined chemically. In addition, two new putative toxins called Pn4A and Pn4B were characterized and their predicted complete amino acid sequence revealed approximately 78% similarity to Tx4(6-1).

Quality protein maize: a biochemical study of enzymes involved in lysine metabolism.

Quality protein maize (QPM) varieties have been produced by the introduction of opaque-2 modifier genes. Two QPM varieties, BR451 and BR473, a wild type and an opaque-2 variety, have been used to study key enzymes controlling lysine metabolism in the endosperm during development. Aspartate kinase and homoserine dehydrogenase enzymes, which are involved in lysine and threonine biosynthesis, respectively, exhibited identical activity patterns during endosperm development, with a maximum specific activity at 16 days after pollination. The QPM varieties exhibited higher levels of aspartate kinase activity in the endosperm, suggesting an increased rate of lysine biosynthesis when compared to the opaque-2 and wild-type genotypes. Similar results were observed for the lysine ketoglutarate reductase and saccharopine dehydrogenase enzymes, which form a single bifunctional polypetide involved in endosperm lysine degradation. Both enzyme activities were strongly reduced in the opaque-2 maize variety when compared to the wild-type maize, whereas the QPM varieties exhibited even lower levels of lysine ketoglutarate reductase-saccharopine dehydrogenase activities when compared to the opaque-2 variety. The developmental pattern of enzyme activity showed a different profile when compared to the enzymes involved in lysine biosynthesis, with activity being detected only 12-16 days after pollination (DAP) and maximum activities approximately 24 DAP. These results also suggest that the modifier genes have intensified the effect of the opaque-2 mutation on lysine ketoglutarate reductase-saccharopine dehydrogenase. These alterations lead to an increase in soluble lysine in the endosperm of the QPM varieties when compared to the opaque-2 and wild type.

Identification in Portugal and Brazil of a mtDNA lineage containing a 9-bp triplication of the intergenic COII/tRNALys region.

Although the deletion of one of the 9-bp repeats in region V of mitochondrial DNA is very common in Asians, Asian-derived populations and Africans, the triplication of the 9-bp segment was described only a few times, mostly on individuals from Asian origin. Here, we report for the first time the presence of the 9-bp triplication in Europeans. The triplication was initially found in one Brazilian individual. Sequencing of the hypervariable segments I (HVSI) and II (HVS2) of the control region and RFLP analysis of the coding region classified the mtDNA as belonging to the European haplogroup H. Since white Brazilians are predominantly of Portuguese descent, we screened 96 unrelated Northern Portuguese for the 9-bp triplication and found its presence in two of them (2.1%). One of these had an mtDNA haplotype identical to that of the Brazilian individual, while the other differed in a single base change in HVS2. The fact that the 9-bp triplication has reached polymorphic frequencies in Northern Portugal and that it has apparently differentiated into at least two lineages defined by the mutuation in HVS2 suggests that it probably occurred a long time ago.

Cloning of cDNAS encoding neurotoxic peptides from the spider Phoneutria nigriventer.

A cDNA library made from venom glands of the spider Phoneutria nigriventer was constructed and used to clone neurotoxic peptides. A cDNA of about 360 nucleotides encoding the precursor for the toxin Tx2-1 active on mammals has been isolated. The deduced amino acid sequence for the mature polypeptide confirms the polypeptide sequence previously published. In addition, two new putative toxins called Pn2-1A and Pn2-5A have been characterized and their complete amino acid sequence show 92% similarity to Tx2-1 and 94% similarity to Tx2-5 respectively. The cDNAs revealed that the precursors contain signal peptides characterized by a very hydrophobic core and a propeptide interposed between the signal sequence and the peptide toxin.

Diallel among twenty eight varieties of maize

Twenty eight varieties of maize of different maturities and types of endosperm were assessed together with 378 F(1), and seven commercial hybrids (controls) in three locations: Sete Lagoas, MG, Goiânia, GO, and Londrina, PR. The varieties represent germplasms adapted to different areas of Brazil,used in the breeding program at the National Maize and Sorghum Research Center at Sete Lagoas, MG. The joint analysis of variance for ear weight showed significance (P < O.O1) for environments, entries, varieties, heterosis, mean heterosis, variety heterosis, specific heterosis, environments x entries and environments x varieties. The average yield of the varieties varied from 2,322 to 7,704 kg/ha, while for the intervatietal hybrids the variation was from 4,112 to 8,363 kg/ha. The mean heterosis was 489 kg/ha and the varietal heterosis varied from -589 to 1,339 kg/ha. The highest specific heterosis was obtained for the BR 105 x BA III - Tusón crossing. Some intervarietal hybrids were higher yielding than the best control. This is promising for breeding purposes, since new synthetic varieties can be formed or used to begin programs to produce hybrids. No association was found between heterosis and endosperm type.