Genetics of stem rust resistance in four popular durum wheat cultivars

A study was conducted to understand the mode of inheritance and extent of diversity of stem rust resistance in four popular durum wheat cultivars of central India viz., HI 8498 (Malav Shakti), HI 8663 (Poshan), HI 8713 (Pusa Mangal) and HI 8737 (Pusa Anmol) using Puccinia graminis tritici (Pgt) pathotypes 15-1 (123G15) and 40-3 (127G29). These cultivars were crossed with susceptible parents i.e., Motia and Malvi Local and were also crossed among themselves in half diallel fashion. The F2 and F3 segregation data revealed that a single dominant gene each controlled resistance to the pathotype 40-3 in HI 8713 and HI 8663, while two dominant genes each governed resistance to this pathotype in HI 8737 and HI 8498. A single dominant gene each conditioned resistance to the pathotype 15-1 in all the four cultivars. The F2 segregation data of the intercrosses among the resistant parents showed that three different resistance genes controlled resistance among four cultivars against each Pgt pathotype 40-3 and 15-1. These genes seem to be different from the most commonly postulated stem rust resistance genes in Indian durum wheat germplasm viz., Sr11, Sr12, Sr7b and Sr9e which are ineffective/less effective against the test pathotypes. Hence, the genes identified in the present study can be utilized in broadening the genetic base of stem rust resistance in Indian durum wheat.

CNVmap: A Method and Software To Detect and Map Copy Number Variants from Segregation Data

Single nucleotide polymorphisms (SNPs) are used widely for detecting quantitative trait loci, or for searching for causal variants of diseases. Nevertheless, structural variations such as copy-number variants (CNVs) represent a large part of natural genetic diversity, and contribute significantly to trait variation. Numerous methods and softwares based on different technologies (amplicons, CGH, tiling, or SNP arrays, or sequencing) have already been developed to detect CNVs, but they bypass a wealth of information such as genotyping data from segregating populations, produced, e.g., for QTL mapping. Here, we propose an original method to both detect and genetically map CNVs using mapping panels. Specifically, we exploit the apparent heterozygous state of duplicated loci: peaks in appropriately defined genome-wide allelic profiles provide highly specific signatures that identify the nature and position of the CNVs. Our original method and software can detect and map automatically up to 33 different predefined types of CNVs based on segregation data only. We validate this approach on simulated and experimental biparental mapping panels in two maize populations and one wheat population. Most of the events found correspond to having just one extra copy in one of the parental lines, but the corresponding allelic value can be that of either parent. We also find cases with two or more additional copies, especially in wheat, where these copies locate to homeologues. More generally, our computational tool can be used to give additional value, at no cost, to many datasets produced over the past decade from genetic mapping panels.

CNVmap: a method and software to detect and map copy number variants from segregation data

Single nucleotide polymorphisms (SNPs) are widely used for detecting quantitative trait loci or for searching for causal variants of diseases. Nevertheless, structural variations such as copy-number variants (CNVs) represent a large part of natural genetic diversity and contribute significantly to trait variation. Over the past decade, numerous methods and softwares have been developed to detect CNVs. Such approaches are based on exploiting sequencing data or SNP arrays, but they bypass a wealth of information such as genotyping data from segregating populations, produced e.g. for QTL mapping. Here we propose an original method to both detect and genetically map CNVs using mapping panels. Specifically, we exploit the apparent heterozygous state of duplicated loci: peaks in appropriately defined genome-wide allelic profiles provide highly specific signatures that identify the nature and position of the CNVs. Our original method and software can detect and map automatically up to 33 different predefined types of CNVs based on segregation data only. We validate this approach on simulated and experimental bi-parental mapping panels in two maize and one wheat populations. Most of the events found correspond to having just one extra copy in one of the parental lines but the corresponding allelic value can be that of either parent. We also find cases with two or more additional copies, especially in wheat where these copies locate to homeologues. More generally, our computational tool can be used to give additional value, at no cost, to many datasets produced over the past decade from genetic mapping panels.

Brain calcifications and PCDH12 variants

Objective:To assess the potential connection between PCDH12 and brain calcifications in a patient carrying a homozygous nonsense variant in PCDH12 and in adult patients with brain calcifications.Methods:We performed a CT scan in 1 child with a homozygous PCDH12 nonsense variant. We screened DNA samples from 53 patients with primary familial brain calcification (PFBC) and 26 patients with brain calcification of unknown cause (BCUC).Results:We identified brain calcifications in subcortical and perithalamic regions in the patient with a homozygous PCDH12 nonsense variant. The calcification pattern was different from what has been observed in PFBC and more similar to what is described in in utero infections. In patients with PFBC or BCUC, we found no protein-truncating variant and 3 rare (minor allele frequency <0.001) PCDH12 predicted damaging missense heterozygous variants in 3 unrelated patients, albeit with no segregation data available.Conclusions:Brain calcifications should be added to the phenotypic spectrum associated with PCDH12 biallelic loss of function, in the context of severe cerebral developmental abnormalities. A putative role for PCDH12 variants remains to be determined in PFBC.

Inheritance of Spear-Shaped Leaf in Peanut

ABSTRACT Recently, a single Spear-shaped Leaf mutant plant was discovered in the ‘Georgia-06G' peanut (Arachis hypogaea L. ssp. hypogaea var. hypogaea) cultivar. The mutant had narrow leaflets with each leaflet tapering to a point which gives the appearance of a spearhead shape. Three cross combinations were used to determine the inheritance of this new mutant. F1, F2, and F3 segregation data strongly supported a single incompletely dominant gene, designated SpL, controlling the inheritance of the Spear-shaped Leaf trait. The F2:3 homozygous spear-shaped individual plants had taller mainstem heights, narrower leaflet width, reduced pod weight, and lower SMK percentages compared to the F2:3 homozygous normal leaf plants resulting from the same closely related cross combination (Georgia-06G x Spear-shaped Leaf mutant).

Southern Blight (Sclerotium rolfsiiSacc.) of Cowpea: Genetic Characterization of Two Sources of Resistance

Field studies were conducted to characterize the genetic nature of resistance to southern blight (caused bySclerotium rolfsiiSacc.) exhibited by the cowpea [Vigna unguiculata(L.) Walp.] cultivars Carolina Cream and Brown Crowder and to determine if a genetic relationship exists for this resistance between the two cultivars. Examination of the comparative frequency distributions of the parental and progeny populations of the “Carolina Cream” x “Magnolia Blackeye” and “Brown Crowder” x “Magnolia Blackeye” crosses and the corresponding segregation data indicates that the southern blight resistances exhibited by “Carolina Cream” and “Brown Crowder” are conditioned by single dominant genes. Examination of the segregation data from the parental and progeny populations of the “Carolina Cream” x “Brown Crowder” cross suggests that the two resistance genes are not allelic. The availability of each of the resistance genes in cultivar-type genetic backgrounds should allow for rapid incorporation of southern blight resistance genes into other cowpea cultivars by the application of conventional plant breeding methodologies.