The Multigeneic _Rhg1_ Locus: A Model For The Effects on Root Development, Nematode Resistance and Recombination Suppression.

Soybean (Glycine max L. Merr.) resistance to populations (HgType) of _Heterodera glycines I._, the soybean cyst nematode (SCN), requires a functional allele at rhg1. An apoptosis-like response in the giant cells formed around the nematode results 24-48 h after feeding commences. This study aimed to identify the role of the three genes within the rhg1 locus, a receptor like kinase (RLK), a laccase and an ion anti-porter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles. Features of the rhg1 locus, the candidate genes and their nascent transcripts and proteins in roots were elucidated. First, evidence for a syntenic gene cluster was found and the effectiveness of SNP probes for distinguishing the homeolog sequence variant on linkage group (Lg) B1 from alleles at the rhg1 locus on Lg G was shown. Analysis of plant s heterozygous at rhg1 showed that the allele for resistance was dominant. The absence of recombination events among the NILs between the RLK and other 2 genes eliminated the possibility of a monogeneic rhg1 locus. Finally, an effect on root development was discovered. A model for multigeneic resistance based on developmental control of root growth including a mechanism for segregation distortion is presented

Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

<p>Abstract</p> <p>Background</p> <p>Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (<it>Glycine max</it>) genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS). Here the aim was to use BAC end sequences (BES) derived from three minimum tile paths (MTP) to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches.</p> <p>Results</p> <p>Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs) were single nucleotide polymorphisms (SNPs; 89%) and single nucleotide indels (SNIs 10%). Larger indels were rare but present (1%). Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed.</p> <p>Conclusion</p> <p>The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de-convolution and positioning of sequence scaffolds (see BES_scaffolds section of SoyGD). This approach will assist genome annotation for paleopolyploid and true polyploid genomes such as soybean and many important cereal and fruit crops.</p

Resistance to Soybean Cyst Nematode: Rhg1

The genes underlying rhg1 lie at a sometimes dominant sometimes co-dominant locus, necessary for resistance to all Hg types of the soybean (Glycine max (L.) Merr.) cyst nematode (Heterodera glycines). Genomic research identified; nucleotide changes within a candidate gene encoding a receptor like kinase (RLK) that were capable of altering root development and thereby part of the resistance to Hg types 0 (race 3); changes in a laccase that are capable of altering cyst development; and genes underlying changes in membrane biology. This set of three genes are subject to co-selection with a modifier locus on another linkage block. Root development is slowed in the resistant seedling and results in end of season yield loss when SCN is not present. However, in the presence of SCN resistant seedling roots grow just as vigorously as the now slower growing parasitized susceptible roots and therefore show little loss to SCN parasitism. In some genotypes but not others the RLK can act alone to confer resistance. Functional paralogs of the three gene cluster have been found on other linkage groups including A1, B1, G, and O and these can be functional in different sources of resistance like G. soja, PI 437654 and PI438489B. At rhg1 the allele differences change the structure, interacting partners and activity of the LRR protein and the laccase. The changes between the alleles result in about 30 other proteins (judged by 2 D gels), 112 metabolites (by FTICRMS) and 8 metabolites (by GCMS) to increase in abundance in roots during SCN infection in the resistant NILs. Understanding the basis of root stunting by resistance alleles will be used to improve methods for developing new nematode resistant soybean cultivars that do not suffer from the yield suppression and low seed germination rates of existing cultivars

Validation of molecular markers linked to low glucosinolate QTLs for marker assisted selection in Indian mustard (Brassica juncea L. Czern & Coss)

Not AvailableSix earlier reported markers closely linked to low glucosinolate QTLs of Brassica juncea, spread across ‘A’ genome (A2, A3 and A9) were validated in a recombinant inbred line (RIL) population of a cross between Pusa Mustard-21 (low erucic acid) and EC-597325 (double low) genotypes, to utilize them in marker-assisted selection (MAS). Of them, four markers viz., GER 1 amplified alleles of 650 bp and of 950 bp, GER 5 amplified 310 bp and 350 bp, At5gAJ67 amplified 500 bp and 450 bp and Myb28 amplified alleles of size 900 bp and 920 bp in EC597325 and Pusa Mustard-21, respectively and therefore differentiated low and high glucosinolate parents. These four polymorphic markers were then used to genotype the phenotyped RIL population consisting 608 plants. Marker-trait association was tested for goodness of fit using c2 test. Of the four markers, GER1 and GER5 showed higher phenotypic variance (R2 value) compared to the others, indicating their significance in determination of glucosinolates and prospects for use in MAS for development of Indian mustard genotypes with low glucosinolates content.Not Availabl

Molecular Strategies for Developing Salt Tolerant Crops

121-137Salinity is one of the most important abiotic stresses for agricultural crops. High concentrations of salts cause hyperosmotic and ionic stresses, which, in turn, may generate secondary stresses such as oxidative stress, etc. The complexity and polygenic nature of salt tolerance trait has seriously limited the efforts to develop salt-tolerant crop varieties. This paper reviews new molecular strategies that have been or can be used for the molecular dissection of plant responses to salt stress, discovery of novel structural and regulatory genes involved in stress adaptation, and transgenic and molecular marker strategies used for engineering salt tolerance in plants. Application of novel techniques such as genome sequencing, high-throughput analysis of genomic-scale expressed sequence tags (ESTs), DNA chips/cDNA microarray analyses, targeted or random mutagenesis, knockouts, molecular mapping and gain-of-function or mutant complementation, is expected to accelerate the discovery of the new genes involved in stress adaptation as well as improve understanding of stress biology. A number of stress-related genes have been characterized including the ones that encode for important enzymes or a biochemical pathway, participate in signaling pathways or act as transcriptional regulators for coordinated regulation of stress related genes. Some of these genes have been successfully transferred in model plant species including Arabidopsis, rice and tobacco, and a marginal to significant improvement in salt-tolerance has been reported. In addition, molecular markers can be used for linkage mapping of genes/QTLs for salinity tolerance trait, marker-assisted transfer and pyramiding of such QTLs into agronomically desirable genotypes and/or for map-based cloning of genes. Application of transgenic and molecular marker research coupled with rapid gene discovery via functional genomic research in plants shall provide effective means for designing salt-tolerant crops.</span

Molecular strategies for developing salt tolerant crops

Salinity is one of the most important abiotic stresses for agricultural crops. High concentrations of salts cause hyperosmotic and ionic stresses, which, in turn, may generate secondary stresses such as oxidative stress, etc. The complexity and polygenic nature of salt tolerance trait has seriously limited the efforts to develop salt-tolerant crop varieties. This paper reviews new molecular strategies that have been or can be used for the molecular dissection of plant responses to salt stress, discovery of novel structural and regulatory genes involved in stress adaptation, and transgenic and molecular marker strategies used for engineering salt tolerance in plants. Application of novel techniques such as genome sequencing, high-throughput analysis of genomic-scale expressed sequence tags (ESTs), DNA chips/cDNA microarray analyses, targeted or random mutagenesis, knockouts, molecular mapping and gain-of-function or mutant complementation, is expected to accelerate the discovery of the new genes involved in stress adaptation as well as improve understanding of stress biology. A number of stress-related genes have been characterized including the ones that encode for important enzymes or a biochemical pathway, participate in signaling pathways or act as transcriptional regulators for coordinated regulation of stress related genes. Some of these genes have been successfully transferred in model plant species including Arabidopsis, rice and tobacco, and a marginal to significant improvement in salt-tolerance has been reported. In addition, molecular markers can be used for linkage mapping of genes/QTLs for salinity tolerance trait, marker-assisted transfer and pyramiding of such QTLs into agronomically desirable genotypes and/or for map-based cloning of genes. Application of transgenic and molecular marker research coupled with rapid gene discovery via functional genomic research in plants shall provide effective means for designing salt-tolerant crops

Identification of microsatellite markers for differentiating some Basmati and non-Basmati rice varieties

519-526Microsatellite marker (SSR) analysis was used to differentiate premium traditional Basmati rice varieties from other cheaper cross-bred Basmati/long-grain rice varieties and monitor the cases of adulteration in milled rice samples. Thirteen rice cultivars (4 commercial traditional Basmati, 6 cross-bred Basmati and 3 non-Basmati varieties) were evaluated for allelic diversity using 35 SSR markers. A total of 123 alleles (79-345 bp) were detected; 25 of these were present in Basmati rice varieties only. Polymorphism information content (PIC) value, which is indicative of level of polymorphism, varied from 0.0 (RM167) to 0.858 (RM252), with an average value of 0.447. SSR analysis generated polymorphism sufficient to differentiate all the 13 rice genotypes. Of the 35 markers, 16 showed amplification of a different allele in one or more of the traditional/cross-bred Basmati rice varieties than in IR36 (indica) and Azucena (japonica). Some SSRs (RM60, RM84, RM252, RM171, and RM257) were found unique among the closely related traditional Basmati rice varieties. Traditional Basmati rice varieties could be differentiated from one or more of the cross-bred Basmati rice varieties by allelic polymorphism at 27 of the 35 SSR loci; the most useful markers being RM171, RM1, RM44, RM110, RM229, RM234, RM242, and RM255. Rice varieties were clustered in three groups (indica, japonica, Basmati groups), which correspond well to their known pedigree data. This paper provides effective means to the Basmati traders for varietal differentiation and monitoring adulteration cases using milled rice samples

Not Available

Not AvailableIntroduction Food-based approach is a sustainable and cost-effective option to counter micronutrient malnutrition in public health particularly in poor communities. The present study aimed to develop F1 hybrids from early-and mid-maturity groups of Indian cauliflower rich in essential dietary nutrients. Materials and methods Cytoplasmic male sterility (CMS) based 50 F1 hybrids (10 CMS lines × 5 testers) from early-maturity group and 20 F1 crosses (5 CMS lines × 4 testers) from mid-maturity group were generated in line × tester mating design and evaluated in randomized block design in respective maturity groups in 2020–21. Eight dietary minerals content were analysed in curd portion using atomic absorbance spectrophotometer and sulphur by barium sulphate turbidimetry method. Results The CMS lines, fertile inbred lines and F1 crosses from both maturity groups showed significant variation in minerals content. Best combiners for minerals in early group were CMS 999–41–5 (Fe, Mn, Mg, Ca, S) and CMS 4348–41–5 (Zn, Na) in CMS lines while DC 98–2 (Cu, Ca) and DC 67 (Zn, Mn, Na) among the testers. In mid group, CMS 8401 (Fe, Na, Ca, K) and CMS 1944–309 (Zn, S) CMS lines and DC 401 (Fe, S, K) and DC 476 (Cu, Mn, Na) testers were good combiners. The best heterotic hybrids in early group were CEH35 for Fe, CEH27 for Zn and Na, CEH38 for Cu and Mn and CEH43 for Ca. In mid group, CMH2 was most heterotic for Fe and Mn and CMH4 for Ca content.Not Availabl