M. V. C. Gowda

Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes.

The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)4×, were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.

An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.)

Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01–a10 and b01–b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut.

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.

Characterization of AhMITE1 transposition and its association with the mutational and evolutionary origin of botanical types in peanut (Arachis spp.)

AhMITE1 is an active miniature inverted repeat transposable element (MITE) in peanut (Arachis hypogaea L). Its transpositional activity from a particular (FST1-linked) site within the peanut genome was checked using AhMITE1-specifc PCR, which used a forward primer annealing to the 5′-flanking sequence and a reverse primer binding to AhMITE1. It was found that transposition activation was induced by stresses such as ethyl methane sulfonate (EMS), gamma irradiation, environmental conditions, and tissue culture. Excision and insertion of AhMITE1 at this particular site among the mutants led to gross morphological changes resembling alternate subspecies or botanical types. Analysis of South American landraces revealed the presence of AhMITE1 at the site among most of the spp. fastigiata types, whereas the element was predominantly missing from spp. hypogaea types, indicating its strong association. Four accessions of the primitive allotetraploid, A. monticola were devoid of AhMITE1 at the site, indicating only recent activation of the element, possibly because of the “genomic shock” resulting from hybridization followed by allopolyploidization.

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.

Mechanisms of Resistance to Tobacco Cutworm (Spodoptera litura F.) and their Implications to Screening for Resistance in Groundnut

SummaryThe Tobacco cut worm (Spodoptera litura Fab.), a polyphagous defoliating insect is a major pest on groundnut in Asia. Screening germplasm for resistance to Spodopteralitura in the field under high infestation revealed significant genotypic variation. Low damage was observed on Mutant (28-2), NC Ac 343, ICGV 86031, R 9227 and TAG 24. In the laboratory rearing of insect, the resistant genotypes, NC Ac 343, Mutant 28-2 and R 9227 affected larval growth and survival, pupal development, adult emergence and fecundity indicating antibiosis as the principal mechanism of resistance. The reduction in larval weight reared on ICGV 86031 could be due to the toughness of leaves. Though the genotype TAG 24 suffered low damage in the field, the larval and pupal development was normal in the laboratory revealing avoidance/non-preference as the mechanism of resistance. Based on the insight gained from the growth and development of the insect on resistant genotypes, the gain in weight (GIW) of the pre-starved larvae was assessed for its suitability in rapid screening. GIW in 24 h by III instar larvae fed with fully expanded II leaf was found suitable in screening for resistance based on antibiosis. The method could be adopted for screening large breeding populations in a short time under laboratory conditions. The resistant genotypes with different mechanisms of resistance could be hybridized to pool the resistant genes for enhancing the level and effectiveness of resistance in the management of the pest.

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.

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.