QTL‐seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)

Rust and late leaf spot (LLS) are the two major foliar fungal diseases in groundnut, and their co‐occurrence leads to significant yield loss in addition to the deterioration of fodder quality. To identify candidate genomic regions controlling resistance to rust and LLS, whole‐genome resequencing (WGRS)‐based approach referred as ‘QTL‐seq’ was deployed. A total of 231.67 Gb raw and 192.10 Gb of clean sequence data were generated through WGRS of resistant parent and the resistant and susceptible bulks for rust and LLS. Sequence analysis of bulks for rust and LLS with reference‐guided resistant parent assembly identified 3136 single‐nucleotide polymorphisms (SNPs) for rust and 66 SNPs for LLS with the read depth of ≥7 in the identified genomic region on pseudomolecule A03. Detailed analysis identified 30 nonsynonymous SNPs affecting 25 candidate genes for rust resistance, while 14 intronic and three synonymous SNPs affecting nine candidate genes for LLS resistance. Subsequently, allele‐specific diagnostic markers were identified for three SNPs for rust resistance and one SNP for LLS resistance. Genotyping of one RIL population (TAG 24 × GPBD 4) with these four diagnostic markers revealed higher phenotypic variation for these two diseases. These results suggest usefulness of QTL‐seq approach in precise and rapid identification of candidate genomic regions and development of diagnostic markers for breeding applications.     

Molecular tagging of a rust resistance gene in cultivated groundnut (Arachis hypogaea L.) introgressed from Arachis cardenasii

Rust is a serious and the most prevalent groundnut disease in tropical and subtropical growing regions of the world. A total of 164 recombinant inbred lines derived from resistant (VG 9514) and susceptible (TAG 24) cultivated groundnut parents were screened for rust resistance in five environments. Subsequent genotyping of these lines with 109 simple sequence repeat (SSR) markers generated a genetic linkage map with 24 linkage groups. The total length of the linkage map was 882.9 cM with an average of 9.0 cM between neighbouring markers. The markers pPGPseq4A05 and gi56931710 flanked the rust resistance gene at map distances of 4.7 cM and 4.3 cM, respectively, in linkage group 2. The significant association of these two markers with the rust reaction was also confirmed by discriminant analysis. The informative SSR markers classified rust-resistant and susceptible groups with 99.97% correctness. The SSR markers pPGPseq4A05 and gi56931710 were able to identify all the susceptible genotypes from a set of 20 cultivated genotypes differing in rust reaction. Tagging of the rust resistance locus with linked SSR markers will be useful in selecting the rust resistant genotypes from segregating populations and in introgressing the rust resistance genes from diploid wild species.     

Inheritance of resistance to groundnut rosette virus in groundnut (Arachis hypogaea L.)

A method of field screening groundnut seedlings for resistance to groundnut rosette virus (GRV), by means of which over 97% incidence was induced in rows of susceptible test plants, was developed at Chitedze Research Station in Malawi. Two GRV-resistant Virginia cultivars (RG 1 and RMP 40) were crossed with three susceptible cultivars, one from each of the Spanish (JL 24), Valencia (ICGM 48) and Virginia (Mani Pintar) botanical groups. Twelve F₁ reciprocal crosses and their F₂ and backcross generations were produced and the material screened in nurseries in 1985/86 and 1986/87. Seedlings raised from plants which did not become infected in the field were inoculated in the glasshouse in order to eliminate susceptible escapees. The numbers of diseased and healthy individuals in each population were subjected to χ² tests. In the majority of the F₂ populations a good fit was obtained for a ratio of one resistant to 15 susceptible plants, a ratio to be expected if resistance to GRV were determined by a pair of independent complementary recessive genes. This was further supported by data from backcross generations.     

Diallel analysis in groundnut (Arachis hypogaea L.)

Summary An 8 × 8 full diallel experiment based on 4 bunch plus 4 spreading types of groundnut (Arachis hypogaea L.) was conducted over three environments. For both number of pods and pod yield, additive, nonadditive and reciprocal cross effects were detected and these were also influenced by changes in environments. For number of pods additive genetic variance was predominant whereas it was approximately equal to non-additive genetic variance for pod yield. Graphical analysis revealed the presence of strong non-allelic interaction for number of pods whereas for pod yield absence of dominance and/or presence of non-allelic interaction was evident.Part of Ph.D. Thesis of the first author     

Origins of resistances to rust and late leaf spot in peanut (Arachis hypogaea,Fabaceae)

The cultivated peanut (Arachis hypogaea, Fabaceae) is believed to have originated along the eastern slopes of the Andes in Bolivia and northern Argentina. The crop is now grown throughout tropical and warm temperate regions. Among diseases attacking peanuts, rust caused byPuccinia arachidis and late leaf spot caused byPhaeoisariopsis personata are the most important and destructive on a worldwide scale. Both pathogens, restricted in host range to Arachis, probably originated and coevolved in South America along with their hosts. In recent years there has been much emphasis on screening of peanut germplasm for resistance to these diseases. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISA T), India, some 10,000 peanut germplasm accessions were screened for resistance to rust and late leaf spot during 1977–1985 and sources of resistance indentified for either or both pathogens. Of the resistant genotypes, about 87% belonged to A. hypogaea var.fastigiata and 13% to var.hypogaea; 84% originated in South America or had South American connections. A high percentage (75%) had their origin in Peru (believed to be a secondary gene center for var.hirsuta and var.fastigiata,), suggesting that resistance to rust and late leaf spot diseases might have evolved in that country.     

Enhanced cross pollination to widen the scope of breeding in groundnut (Arachis hypogaea L.)

Summary Six groundnut genotypes belonging to the Virginia and Valencia sub-groups were irradiated with gamma rays at doses of 5, 10, 15 and 20 kR, much below LD₅₀, and grown surrounded by a pollen parent in a split-plot design. The succeeding two generations were checked for the occurrence of hybrids by examining the segregation for pod and seed characteristics and the two quantitative characters, pod and seed yield. Cross-pollination up to 20.8% was observed in M13, a Virginia cultivar. There was a genotype-dose interaction for the extent of cross-pollination. Cross-pollination was higher in Virginia than Valencia genotypes and more frequent under 15 and 20 kR than under other doses, in general. The observed substantial enhancement of cross-pollination encourages the use of seed irradiation at proper doses as a method for increasing recombination in plant breeding programmes.     

Early generation intermating for yield improvement in groundnut (Arachis hypogaea L.)

Summary Seeds of 4 crosses of groundnut (Arachis hypogaea L.), Robut 33-1 x Chico, Robut 33-1 x NC Ac 17090, Robut 33-1 x PI 298115 and MK 374 x GAUG 1, were irradiated with 30 kR. In the F₁, some branches of each plant were intermated with other plants at random and others selfed in each cross to produce S₂ and F₂ seeds. They were evaluated for pod yield, shelling percentage and 100-kernel weight. The frequency of plants superior to F[in1] was much higher in S₂ than in F₂, which was, in general, true for the values of yield and its components. The S₂ and F₂ were advanced to third generation by selfing. The families descending from S₂ showed clear superiority over those from F₂. The reason for such superiority was suggested to be the recombination of genes from the upper and lower ends of the genotypic distribution under intermating.     

Root turnover of groundnut (Arachis hypogaea L.) in soil tubes

Five groundnut cultivars were grown in transparent tubes of pasteurized loam compost in growth-chamber conditions. Weekly tracings were made of all the roots visible through the walls of the tubes. White roots were assessed as living, and brown or decayed roots as dead; this correlated with microscopical assessments of root viability based on cytoplasmic staining with neutral red followed by plasmolysis.For all five cultivars, root laterals began to die 3–4 weeks after plants were sown. Death of root laterals progressed down the soil profile with time, while new roots were produced successively deeper from the extending taproot. The half-life of individual roots was calculated as 3.7–4.4 weeks for all cultivars, based on assessments of the roots that died up to plant maturity (14–20 weeks, depending on cultivar). At maturity, 73–83% of the cumulative length of root systems had died. The onset and rate of root death were not related to onset of flowering or pod-filling; instead, the peak times of root death at different distances down the root system were related to earlier (3–5 week) peak times of root production in those regions. The net result of root turnover was that, despite continued new root production, the maximum length of living (white) roots of each cultivar was recorded at 2–4 weeks after sowing. Death of the earliest formed root laterals was also observed in the first five weeks after sowing of groundnut in an experimental field plot in Malawi. Progressive root turnover is considered to be a normal feature of groundnut, perhaps representing an energy-economy strategy.     

Pod development of groundnut (Arachis hypogaea L.) in solution culture

Normal pods (containing seed) of groundnut (Arachis hypogaea L.) (cv. TMV-2) were successfully raised in darkened, aerated, nutrient solution, but not in the light. The onset of podding was evident 7 to 8 d after gynophores were submerged in the darkened nutrient solution. An examination of pods and submerged portions of gynophore surfaces by scanning electron microscopy showed the presence of two distinctly different protuberances: unicellular root-hair-like structures that first developed from epidermal cells of the gynophores and developing pods; and branched septate hairs that developed later from cells below the epidermal layer. The septate hairs became visible only after the epidermal and associated unicellular structures had been shed by the expanding gynophore and pods. Omission of Mn and Mg from the podding environment increased pod and seed weight, whilst omission of Zn reduced pod and seed weight.     

Genetic variation for VA mycorrhiza-dependent phosphate mobilisation in groundnut (Arachis hypogaea L.)

Nine cultivars of groundnut (Arachis hypogaea L.) were grown in a soil poor in available N or P. There was clearly genetic variation of characteristics indicative of VA mycorrhiza-dependent phosphate mobilisation, namely, VA mycorrhiza fungal spore count (SC), percentage of infection (IF) by VA mycorrhizal fungi (VAMF) and acid and alkaline phosphatase activities. Among the cultivars, one was non-nodulating with low values for all characteristics and in another experiment, this non-nodulating cultivar, one of its parents (PI 259747), a national check (Robut 33-1) and the highest yielding cultivar among the original nine (NFG 7), were grown and investigated for various P-mobilising properties and yield. The linear regression coefficient of pod yield on % VAMF infection was significant in both the experiments. Additionally, many of the correlation coefficients of pod yield and VAM dependent characteristics were positive and significant. From consideration of published evidence, it seems possible to breed for the desirable reinforcing effects of infestation, by VAMF and Rhizobium that can ultimately improve the productivity of groundnuts.     

Nonparametric approach to multitrait selection for yield in groundnut (Arachis hypogaea L.)

Summary Eight characters related to nitrogen fixation and pod development measured 30 days after flowering were evaluated for their correct grading of the relative yield performance of 17 genetically diverse lines of groundnut (Arachis hypogaea L.). Each line was assigned a high or low yield status based on its pod yield, shelling percentage, and 100-kernel weight. Seventeen character combinations were examined for their relative merit in correct identification of the yield status of lines. The character sets, nitrogenase activity alone or in combination with nitrogen percent or shoot weight identified the status of 77% of lines correctly. The extent to which various characters accounted for the variation in pod yield was also checked by multiple regression analysis. While the character combination, nitrogen percent plus leaf area explained 75% of variation in pod yield, nodule mass, nitrogenase activity, and leaf area occurred in some other combinations that explained yield variation to a lesser extent. These analyses point to the profitability of involving crop physiological traits such as leaf area and nitrogen percent in selecting for relative yield performance in groundnut.IARI Regional Station, Tutikandi, Simla 171004, IndiaNational Research Center for Groundnut, Timbawadi, Junagadh 362015, India     

RAPD analysis of induced mutants of groundnut (Arachis hypogaea L.)

Radiation-induced mutants of groundnut cv. Spanish Improved showing distinct morphological differences and the parent were screened for RAPD variability. The analysis revealed characteristic band differences among the 12 mutants and the parent. The polymorphic RAPD bands were dominant in the F₁ and segregated in a Mendelian fashion in the F₂. The RAPD technique brought out greater genome variability than RFLP.     

Resistance in groundnut (Arachis hypogaea L.) to Aphis craccivora (Koch).

The behaviour, development and reproductive capacity of Aphis craccivora, vector of a number of groundnut viruses, are compared on a range of susceptible and resistant genotypes. Field trials demonstrated no significant difference between genotypes in the rate of arrival of alates, but population development was slower, and subsequent population decline faster, on the genotype EC 36892 (ICG 5240). Behavioural studies in the screenhouse, likewise showed no inhibition to alighting onto EC 36892 though choice tests demonstrated a significant redistribution of the population in favour of the susceptible genotype TMV 2 (ICG 221) over the following 10 h. In clip cage experiments, development was faster and nymphal numbers were higher on the genotype TMV 2 compared to EC 36892.     

Transgenics in groundnut (Arachis hypogaea L.) expressing cry1AcF gene for resistance to Spodoptera litura (F.)

Large number of primary transgenic events were generated in groundnut by an Agrobacterium mediated, in planta transformation method to assess the efficacy of cry1AcF against the Spodoptera litura. The amplification of required size fragment of 750 bp with npt II primers and 901 bp with cry1AcF gene primers confirmed the integration of the gene. The expression of the cry gene was ascertained by ELISA in T₂ generation, and the maximum concentration of cry protein in transgenic plants reached approximately 0.82 μg/g FW. Further, Southern blot analysis of ten T₂ transgenic plants proved that transgene had been integrated in the genome of all the plants and Northern analysis of the same plants demonstrated the active expression of cry1AcF gene. The highest mean % larval mortalities 80.0 and 85.0 with an average mean % larval mortalities 16.25 (n = 369) and 26.0 (n = 80) were recorded in T₁ and T₂ generations, respectively. Segregation analysis of the selected lines in the T₃ generation demonstrated homozygous nature. This clearly proved that though there is considerable improvement in average mean % larval mortality in T₂ generation, the cry1AcF gene was effective against S. litura only to some extent.     

The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.)

Molecular markers and genetic linkage maps are pre-requisites for molecular breeding in any crop species. In case of peanut or groundnut (Arachis hypogaea L.), an amphidiploid (4X) species, not a single genetic map is, however, available based on a mapping population derived from cultivated genotypes. In order to develop a genetic linkage map for tetraploid cultivated groundnut, a total of 1,145 microsatellite or simple sequence repeat (SSR) markers available in public domain as well as unpublished markers from several sources were screened on two genotypes, TAG 24 and ICGV 86031 that are parents of a recombinant inbred line mapping population. As a result, 144 (12.6%) polymorphic markers were identified and these amplified a total of 150 loci. A total of 135 SSR loci could be mapped into 22 linkage groups (LGs). While six LGs had only two SSR loci, the other LGs contained 3 (LG_AhXV) to 15 (LG_AhVIII) loci. As the mapping population used for developing the genetic map segregates for drought tolerance traits, phenotyping data obtained for transpiration, transpiration efficiency, specific leaf area and SPAD chlorophyll meter reading (SCMR) for 2 years were analyzed together with genotyping data. Although, 2–5 QTLs for each trait mentioned above were identified, the phenotypic variation explained by these QTLs was in the range of 3.5–14.1%. In addition, alignment of two linkage groups (LGs) (LG_AhIII and LG_AhVI) of the developed genetic map was shown with available genetic maps of AA diploid genome of groundnut and Lotus and Medicago. The present study reports the construction of the first genetic map for cultivated groundnut and demonstrates its utility for molecular mapping of QTLs controlling drought tolerance related traits as well as establishing relationships with diploid AA genome of groundnut and model legume genome species. Therefore, the map should be useful for the community for a variety of applications. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effect of brassionosteriods on nodulation and nitrogenase activity in groundnut (Arachis hypogaea L.)

The effect of brassinolide, 24-epibrassinolide and 28-homobrassinolide on nodulation and nitrogenase activity of groundnut was studied. The tested brassinosteroids substantially increased both nodulation and nitrogenase activity.     

A rapid protocol for somatic embryogenesis from immature leaflets of groundnut (Arachis hypogaea L.)

Summary Plant regeneration via somatic embryogenesis was developed in two groundnut varieties. Somatic embryogenesis was induced from immature leaflets on MS medium with different concentrations of the auxins 2,4-dichlorophenoxyacetic acid (2,4-D) or naphthaleneacetic acid (NAA) in combination with 0.5 mg/l of the cytokinin BA. The highest frequency of somatic embryo formation occurred on MS medium fortified with 20 mg 2,4-D per l. Of the two auxins tested individually 2,4-D was more effective for induction of embryogenesis as well as production of embryos. Embryo development and maturation was achieved on MS medium supplemented with N⁶-benzyladenine (BA) (0.5–2.0 mg/l) and 2,4-D (0.5 mg/l). Plant conversion frequency from somatic embryos was highest in presence of 2.0 mg BA per l and 0.5 mg NAA per l. The frequency of embryogenesis and plant regeneration was higher in the VRI-2 cultivar than in the other cultivar tested. Regenerated plants were transferred to soil, grown to maturity, and produced viable seeds.     

Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)

Key message

Successful introgression of a major QTL for rust resistance, through marker-assisted backcrossing, in three popular Indian peanut cultivars generated several promising introgression lines with enhanced rust resistance and higher yield.

Abstract

Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar ‘GPBD 4’ into three rust susceptible varieties (‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’) through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2–3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56–96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes.     

Variation and inheritance of the arachin polypeptides of groundnut (Arachis hypogaea L.)

Summary Variation in the arachin polypeptides of groundnut genotypes was observed by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Three regions could be observed on the electropherogram. Region 1, corresponding to conarachin, did not show any variation; region 2, consisting of arachin acidic subunits, showed variation; region 3, containing the arachin basic subunits, did not show any variation. There are four varietal classes of arachin polypeptide patterns: class A comprised three acidic subunits of arachin of molecular weights 47.5, 45.1 and 42.6 kd and a basic subunit of 21.4 kd; class B, with three acidic subunits of molecular weights 47.5, 45.1 and 41.2 kd and a basic subunit of 21.4 kd; class C of an additive pattern of class A and class B; class D, of two acidic polypeptides of 47.5, 45.1 kd and the basic 21.4 kd subunit. Of the 90 genotypes studied, 73% belong to class A, 15% to class B and 6% each to class C and D. Analysis of F₂ seeds from a cross between class A and class B genotypes showed that the two polypeptides (42.6 kd and 41.2 kd) are coded by nonallelic genes and also revealed that class C and class D patterns arose as a result of hybridisation between class A and class B. A. monticola, the progenitor of A. hypogaea, showed a pattern similar to the additive pattern of class A and class B while some diploid Arachis species had the 41.2 kd polypeptide. Based on arachin polypeptide patterns the probable origin of A. hypogaea has been suggested.