H. L. Nadaf

Genomewide Association Studies for 50 Agronomic Traits in Peanut Using the ‘Reference Set’ Comprising 300 Genotypes from 48 Countries of the Semi-Arid Tropics of the World

Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the ‘reference set’ of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15–20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (pvalue >2.1×10–6) with wide phenotypic variance (PV) range (5.81–90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.

Expressed variants of Δ12-fatty acid desaturase for the high oleate trait in spanish market-type peanut lines

Increasing the oleic to linoleic acid ratio (O/L) in peanut has positiveeffects on peanut quality and its nutritional value. Δ12-Fattyacid desaturases (Δ12-Fad) have been targeted as logicalcandidates controlling the high oleate trait. A previous study using genomicDNA identified an insertion and a polymorphism resulting in an amino acid changeassociated with the high oleate trait in Spanish-type peanut cultivars. Theobjectives of this research were to use RT-PCR to confirm that the SingleNucleotide Polymorphims (SNPs) identified by analysis of genomic DNA wereexpressed, and to determine if expression patterns for Δ12-Fadwere the same in both seeds and leaves. A polymorphic region of theΔ12-Fad containing a series of nucleotide changes wasamplified, cloned, and sequenced from mRNA of 155 clones of two parental linesand their independent derived backcross lines (IDBLs). The latter differed intheir oleic to linoleic ratio. Data indicated that the “A”insertion and the amino acid change were expressed in both leaf and seed tissue of thehigh and low-intermediate O/L genotypes. It is postulated that several copiesof the Δ12-Fad are present in the genome. It is reasonable toconclude that total activity, and ultimately the O/L ratio, is dependent on thenumber of functional copies. The results provide the basis for an assay toscreen for the high O/L ratio at the molecular level. We also report thepresence of another isozyme of Δ12-Fad with high homology tosoybean isozyme 2 that was expressed in seeds.

The role of mutations in intraspecific differentiation of groundnut (Arachis hypogaea L.)

SummaryBased on morphological diversity, cultivated groundnut (Arachis hypogaea L.) is classified into two subspecies (fastigiata and hypogaea) and further into four botanical types (Spanish bunch, Valencia, Virginia bunch and Virginia runner). In a cross between two Spanish cultivars belonging to ssp. fastigiata, a true breeding variant (Dharwad early runner) sharing some characters of both the subspecies was isolated. The variant, on mutagenesis with ethyl methane sulphonate (EMS) yielded a very high frequency of mutants resembling all four botanical types. Some of the mutants produced germinal reversions to Dharwad early runner in later generations indicating genetic instability. While most of the revertants bred true, some of the mutants continued to segregate, wherein each botanical group of mutants produced all other botanical types. A detailed analysis of the breeding behaviour of mutants revealed several unusual features (such as homozygous mutations, mutation outbursts, segregation distortions, somatic mutations and multiple character mutations) that could not be explained through conventional mutation theory. In the light of these findings, the role of mutations in evolutionary differentiation of the crop and the probable mode of their origin have been discussed.

Mapping of important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut (Arachis hypogaea L.)

A mapping population of recombinant inbred lines (RILs) derived from TMV 2 and its mutant, TMV 2-NLM was employed for mapping important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut. Single nucleotide polymorphism and copy number variation using RAD-Sequencing data indicated very limited polymorphism between TMV 2 and TMV 2-NLM. But phenotypically they differed significantly for many taxonomic and productivity traits. Also, the RIL population showed significant variation for a few additional agronomic traits. A genetic linkage map of 1,205.66 cM was constructed using 91 genic and non-genic Arachis hypogaea transposable element (AhTE) markers. Using single marker analysis and QTL analysis, the markers with high phenotypic variance explained (PVE) were identified for branching pattern (32.3%), number of primary and secondary branches (19.9% and 28.4%, respectively), protein content (26.4%), days to 50% flowering (22.0%), content of oleic acid (15.1%), test weight (13.6%) and pod width (12.0%). Three genic markers (AhTE0357, AhTE0391, AhTE0025) with Arachis hypogaea miniature inverted-repeat transposable element (AhMITE1) activity in the genes Araip.TG1BL (B02 chromosome), Aradu.7N61X (A09 chromosome) and Aradu.7065G (A07 chromosome), respectively showed strong linkage with these taxonomic, productivity and quality traits. Since TMV 2 and TMV 2-NLM differed subtly at DNA level, the background noise in detecting the marker-trait associations was minimum; therefore, the markers identified in this study for the taxonomic and productivity traits may be significant and useful in peanut molecular breeding.

Marker detection and genetic analysis for rust resistance of recombinant and backcross inbred lines in groundnut (Arachis hypogaea L.)

The present work was conducted to study the genetic variation and identification of microsatellite markers linked to rust resistance in groundnut. An F6 mapping population and three backcross populations (BC1F4, BC2F3 and BC3F2) were developed from a cross between the susceptible parent GPBD-5 and resistant parent GPBD-4. There were highly significant differences among recombinants for reaction to rust. A little difference was observed between PCV and GCV for reaction to rust. High heritability coupled with high genetic advance as per cent of mean was observed for reaction to rust in F6, and backcross populations. Bulk segregant analysis in the segregating population of GPBD-5 x GPBD-4 indicated TC5A06 to be putatively linked to rust resistance i.e., single marker analysis (SMA). This marker can be used in marker assisted selection for rust resistance in groundnut improvement program.

Genetic analysis for yield, nutritional and oil quality traits in RIL population of groundnut (Arachis hypogaea L.)

A total of 268 recombinant inbred lines (RILs) were evaluated for genetic variability for yield, nutritional and oil quality traits under two consecutive seasons at two locations. Analysis showed that variability exists in the population for the nutritional and oil quality as well as for yield component traits. Majority of the yield components and oil quality traits were governed by additive effects. The nutritional and oil quality traits were not affected by environmental factors and simple phenotypic selection ensures increased performance of the genotypes. Yield components showed moderate to high heritability but with great influence of environment.

Data on identified foliar fungal disease-resistant introgression lines with higher pod and haulm yield testing of LLS and RUST

Introgression lines (ILs) of groundnut with enhanced resistance to rust and late leaf spot (LLS) recorded increased pod and haulm yield testing. Marker-assisted backcrossing (MABC) approach was used to introgress a genomic region containing a major QTL that explains >80% of phenotypic variance (PV) for rust resistance and 67.98% PV for LLS resistance. ILs in the genetic background of TAG-24, ICGV 91114 and JL 24 were evaluated for two seasons (Rainy 2013 and 2014) to select 20 best ILs based on resistance, productivity parameters and maturity duration. Both late leaf spot and rust occur together. while LLS is moderate. infector rows of susceptible variety around the experimental plot and in between test entries ensured uniform spread of disease. The disease scores at ICRISAT, Patancheru . Background genotype, environment and genotype X environment interactions are important for expression of resistance governed by the QTL region. Six best ILs namely ICGV13192, ICGV 13193, ICGV 13200, ICGV 13206, ICGV 13228 and ICGV 13229 were selected with 39–79% higher mean pod yield and 25-89% higher mean haulm yield over their respective recurrent parents. Pod yield increase was contributed by increase in seed mass and number of pods per plant. Experiment location on Google Map

Identified foliar fungal disease-resistant introgression lines with higher pod and haulm yield data in multilocation testing of Groundnut in Dharwad and Aliyar Nagar

Introgression lines (ILs) of groundnut with enhanced resistance to rust and late leaf spot (LLS) recorded increased pod and haulm yield in multilocation testing. Marker-assisted backcrossing (MABC) approach was used to introgress a genomic region containing a major QTL that explains >80% of phenotypic variance (PV) for rust resistance and 67.98% PV for LLS resistance. ILs in the genetic background of TAG-24, ICGV 91114 and JL 24 were evaluated for two seasons (Rainy 2013 and 2014) to select 20 best ILs based on resistance, productivity parameters and maturity duration. Multilocation evaluation of the selected ILs was conducted including disease hot spots. Disease incidence at these two locations is by natural infection wherein, both late leaf spot and rust occur together. The incidence of rust is severe at Aliyarnagar during the season, while LLS is moderate. In all the locations, infector rows of susceptible variety around the experimental plot and in between test entries ensured uniform spread of disease. Only the disease scores at Aliyarnagar, were considered for ANOVA as the scoring at Dharwad-Karnataka was recorded on single replication. Background genotype, environment and genotype X environment interactions are important for expression of resistance governed by the QTL region. Six best ILs namely ICGV13192, ICGV 13193, ICGV 13200, ICGV 13206, ICGV 13228 and ICGV 13229 were selected with 39–79% higher mean pod yield and 25-89% higher mean haulm yield over their respective recurrent parents. Pod yield increase was contributed by increase in seed mass and number of pods per plant. Experiment location on Google Map - Dharwad Experiment location on Google Map - Aliyar Nagar

Identification of main effect and epistatic quantitative trait loci for morphological and yield-related traits in peanut (Arachis hypogaea L.)

An effort was made in the present study to identify the main effect and epistatic quantitative trait locus (QTL) for the morphological and yield-related traits in peanut. A recombinant inbred line (RIL) population derived from TAG 24 × GPBD 4 was phenotyped in seven environments at two locations. QTL analysis with available genetic map identified 62 main-effect QTLs (M-QTLs) for ten morphological and yield-related traits with the phenotypic variance explained (PVE) of 3.84–15.06%. Six major QTLs (PVE > 10%) were detected for PLHT, PPP, YPP, and SLNG. Stable M-QTLs appearing in at least two environments were detected for PLHT, LLN, YPP, YKGH, and HSW. Five M-QTLs governed two traits each, and 16 genomic regions showed co-localization of two to four M-QTLs. Intriguingly, a major QTL reported to be linked to rust resistance showed pleiotropic effect for yield-attributing traits like YPP (15.06%, PVE) and SLNG (13.40%, PVE). Of the 24 epistatic interactions identified across the traits, five interactions involved six M-QTLs. Three interactions were additive × additive and remaining two involved QTL × environment (QE) interactions. Only one major M-QTL governing PLHT showed epistatic interaction. Overall, this study identified the major M-QTLs for the important productivity traits and also described the lack of epistatic interactions for majority of them so that they can be conveniently employed in peanut breeding.

Molecular and Phenotypic Characterization for Leaf Rust Resistance in Bread Wheat (Triticum aestivum L.)

Bread wheat (Triticum aestivum L.) is one of the most important cereal crops worldwide (second after maize), providing staple food for 35 % of the world population. Leaf rust caused by the fungus Puccinia triticina Eriks. is one of the most common foliar diseases of wheat worldwide (Oelke and Kolmer, 2004; Mebrate et al., 2008). Severe leaf rust epidemics can cause yield losses up to 40% (Knott, 1989). Use of resistant wheat cultivars is the most economic and environmentally safe way to reduce losses caused by leaf rust. Till date 71 genes for resistance to leaf rust have been cataloged in wheat (Singh et al., 2012). Most Lr genes confer race-specific seedling resistance and are vulnerable to defeat by new virulent races. Greater durability of resistance could be achieved through combinations of race-specific genes (Kolmer et al., 2008a, 2008b).