Genetics,genomics and breeding of groundnut (Arachis hypogaea L.)

Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker‐assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.     

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

Summary Based 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.     

Identification and inheritance of male sterility in groundnut (Arachis hypogaea L.)

Summary Some plants without pods but with gynophores were observed in two F₄ progenies of two crosses of goundnut (Arachis hypogaea L.). The flowers on these plants had translucent white anthers with no or a few sterile pollen grains. Three such plants in the succeeding generation were hand pollinated with pollen from a short-duration Indian cv. JL 24. The resulting F₁ hybrid plants (male sterile x JL 24) were normal. Chi-square tests for segregation for male fertile and male sterile plants in F₂ and F₃ generations indicated that the male sterility in these crosses of groundnut is governed by two recessive genes. We designate these genes as ms₁ and ms₂ with ms₁ms₁ms₂ms₂ being a male sterile genotype.Submitted as ICRISAT J. A. No. 1812.     

Inheritance of two components of early maturity in groundnut (Arachis hypogaea L.)

Summary Knowledge of inheritance of early maturity or its components is important to groundnut breeders in developing short-duration cultivars. This study was conducted to determine the inheritance of two components of early maturity: days to first flower from sowing, and days to accumulation of 25 flowers from the appearance of first flower, using three groundnut genotypes. Two early-maturing (Chico and Gangapuri) and one late-maturing (M 13) genotypes were crossed in all possible combinations, including reciprocals. The parents, F₁, F₂, F₃, and backcross populations were evaluated for days to first flower from sowing, and for days to accumulation of 25 flowers. The data suggest that days to first flower in the crosses studied is governed by a single gene with additive gene action. Chico and Gangapuri possess the same allele for this component of earliness. Three independent genes with complete dominance at each locus appear to control the days to accumulation of 25 flowers. In crosses between late (M 13) and early (Chico or Gangapuri) parents, a segregation pattern suggesting dominant-recessive epistasis (13 late:3 early) was observed for this component. Segregation in the F₂ generation (1 late:15 early) of both early parents (Chico x Gangapuri) indicated that the genes for early accumulation of flowers in these two parents are at different loci.Submitted as ICRISAT J.A. No. 1557.     

Early generation testing for yield and physiological components in groundnut (Arachis hypogaea L.)

Selection of superior crosses of groundnut (Arachis hypogaea L.) in early generations would increase the probability of identifying superior lines. The objective of this study was to determine the potential of selecting for physiological traits identified in a yield model [crop growth rate (C), reproductive duration (DR) and partitioning (p)] in segregating populations. Forty populations and nine parental lines were evaluated in replicated trials in 1992 (F2, 1993 (F3) and 1994 (F4) at three locations in Niger. Physiological traits were estimated from final yield and biomass as well as data on flowering and maturity. Regressions from two different parent-offspring generations (F2: F3 and F3: F4) were calculated. The results were compared to determine if early generation performance accurately predicts the performance of cross bulks in later generations. Differences were observed among populations and parents for all traits. Effects of locations were significant for C, p and DR in F2 and F3 but nonsignificant for yield and C in F4. Regression coefficients from F3: F2 were 0.10 ± 0.08 for C, 0.45 ± 0.17 for p, 0.10 ± 0.03 for DR and 0.16 ± 0.03 for pod yield. Based on F3: F4 regression, the coefficients were 0.12 ± 0.23 for C, 0.46 ± 0.17 for p and 0.57 ± 0.17 for yield. Parent-offspring correlations were in most cases similar to the regression values. It was concluded that selection for yield and model components in early generation bulks may inneffective. This revised version was published online in July 2006 with corrections to the Cover Date.     

Inheritance of albinism in certain interspecific and intersubspecific crosses in groundnut (Arachis hypogaea L.)

Summary A study of the several interspecific and inter-subspecific crosses indicated that albinism in groundnut is recessive and in these crosses is controlled by triplicate recessive loci.ICRISAT Paper No. JA-336     

RAPD markers linked to a rust resistance gene in cultivated groundnut (Arachis hypogaea L.)

Groundnut rust (Puccinia arachidis Speg.) is an important air borne pathogen, which causes substantial losses in groundnut yield and quality. Although large numbers of accessions were identified as rust resistant in wild, interspecific derivative and cultivated groundnut species, transfer of resistance to well-adapted cultivars is limited due to linkage drag, which worsens yield potential and market acceptance. A F₂ mapping population comprising 117 individuals was developed from a cross between the rust resistant parent VG 9514 and rust susceptible parent TAG 24. Rust resistance was governed by single dominant gene in this cross. We identified 11 (out of 160) RAPD primers that exhibited polymorphism between these two parents. Using a modified bulk segregant analysis, primer J7 (5′CCTCTCGACA3′) produced a single coupling phase marker (J7₁₃₅₀) and a repulsion phase marker (J7₁₃₀₀) linked to rust resistance. Screening of the entire F₂ population using primer J7 revealed that the coupling phase marker J7₁₃₅₀ was linked with the rust resistance gene at a distance of 18.5 cM. On the other hand, the repulsion phase marker J7₁₃₀₀ was completely linked with rust resistance. Additionally, both J7₁₃₀₀ (P = 0.00075) and J7₁₃₅₀ (P < 0.00001) were significantly associated with the rust resistance. Marker J7₁₃₀₀ identified all homozygous rust resistant genotypes in the F₂ population and was present in all the eight susceptible genotypes tested for validation. Thus, J7₁₃₀₀ should be applicable for marker-assisted selection (MAS) in the groundnut rust resistance breeding programme in India. To the best of our knowledge this is the first report on the identification of RAPD markers linked to rust resistance in groundnut.     

Simple sequence repeat markers for botanical varieties of cultivated peanut (Arachis hypogaea L.)

Cultivated peanut (Arachis hypogaea L.) consists of six botanical varieties. Identification of DNA markers associated with botanical varieties would be useful in plant genotyping, germplasm management, and evolutionary studies. We have developed 130 simple sequence repeat (SSR) markers in peanut, 38 of which were used in this study because of their ability in detecting genetic polymorphism among 24 peanut accessions. Eight SSR markers were found useful to classify botanical varieties. Among them, six SSR markers were specific to botanical varieties fastigiata and vulgaris, one to botanical varieties hypogaea and hirsuta, and one to botanical varieties peruviana, and aequatoriana. Also, three of them derived from peanut expressed sequence tags (ESTs) were associated with putative genes. As botanical varieties have different morphological traits and belong to different subspecies in A. hypogaea, these markers might be associated with genes involved in the expression of morphological traits. The results also suggested that SSRs (also called microsatellites) might play a role in shaping evolution of cultivated peanut. Multiplex PCR of botanical variety-specific markers could be applied to facilitate efficient genotyping of the peanut lines.     

Heterosis in relation to genetic divergence and specific combining ability in groundnut (Arachis hypogaea L.)

Summary The frequency and magnitude of heterosis were examined in relation to genetic divergence among parents in two diallel cross experiments in groundnut. The parents were grouped into clusters based on their diver-gence. The range, mean and standard deviation of the intra-and inter-cluster divergence were used to define four divergence classes. The frequency of heterotic crosses and the magnitude of heterosis for yield and its components were found to be higher in crosses between the parents in intermediate divergence classes than extreme ones. The results agreed well with the overall status of the specific combining ability of these crosses.     

Intercropping Studies in Peanut (Arachis hypogaea L.)

With a view to study the effect of intercropping and plant geometries in peanut cv. VRI-1 , a held experiment was conducted at Area Agronomic Centre, Tamil Nadu Co-operative Oilseeds Growers' Federation Limited, Neyveli, India during winter season 1989, (November 89–April 90) under irrigated condition. Three intercrops viz., pigeonpea, sunflower and finger millet were tested at two plant geometries viz., paired rows of 40/20 cm and 45/15 cm. The study indicated that pigeonpea was compatible with peanut and their combination resulted in higher peanut kernel equivalent yield and higher profit. Sunflower and finger millet depressed the base crop yield and found to be unsuitable for intercropping in peanut. Base crop yield was not influenced by the plant geometries.     

SSR analysis of cultivated groundnut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases

Cultivated groundnut (Arachis hypogaea L.) is an agronomically and economically important oilseed crop grown extensively throughout the semi-arid tropics of Asia, Africa and Latin America. Rust (Puccinia arachidis) and late leaf spot (LLS, Phaseoisariopsis personata) are among the major diseases causing significant yield loss in groundnut. The development of varieties with high levels of resistance has been constrained by adaptation of disease isolates to resistance sources and incomplete resistance in resistant sources. Despite the wide range of morphological diversity observed in the cultivated groundnut gene pool, molecular marker analyses have thus far been unable to detect a parallel level of genetic diversity. However, the recent development of simple sequence repeat (SSR) markers presents new opportunities for molecular diversity analysis of cultivate groundnut. The current study was conducted to identify diverse disease resistant germplasm for the development of mapping populations and for their introduction into breeding programs. Twenty-three SSRs were screened across 22 groundnut genotypes with differing levels of resistance to rust and LLS. Overall, 135 alleles across 23 loci were observed in the 22 genotypes screened. Twelve of the 23 SSRs (52%) showed a high level of polymorphism, with PIC values ≥0.5. This is the first report detecting such high levels of genetic polymorphism in cultivated groundnut. Multi-dimensional scaling and cluster analyses revealed three well-separated groups of genotypes. Locus by locus AMOVA and Kruskal–Wallis one-way ANOVA identified candidate SSR loci that may be valuable for mapping rust and LLS resistance. The molecular diversity analysis presented here provides valuable information for groundnut breeders designing strategies for incorporating and pyramiding rust and late leaf spot resistances and for molecular biologists wishing to create recombinant inbred line populations to map these traits.E.S. Mace and D.T. Phong contributed equally to this work.     

Development of genic molecular markers linked to a rust resistance gene in cultivated groundnut (Arachis hypogaea L.)

Development of molecular markers for different economically important traits in cultivated groundnut has progressed at slow pace. Although many genomic SSR markers were developed in both the wild and cultivated groundnut, the genetic linkage map in the species is still not saturated. Availability of a large number of ESTs in GenBank opened up the possibility of integrating new markers and to identify markers closely linked to agronomic traits. EST-SSR markers are also considered as genic molecular markers. In this study, 259 EST-SSR markers were developed by mining 5,184 Arachis hypogaea ESTs from NCBI database. These EST-SSRs and 34 resistance gene candidate markers were used for association and genetic mapping of rust resistance in cultivated groundnut. From these, Cer2, SSR_GO340445, SSR_HO115759, SSR_GO341324 and RGC 2 had a significant association with rust resistance based on locus-by-locus AMOVA and/or Kruskal?CWallis ANOVA. Some of these associated markers also had protein activity related to biotic stress responses. Through genetic mapping, EST-SSR markers SSR_GO340445 and SSR_HO115759 were found closely linked to a rust resistance gene at 1.9 and 3.8?cM distances, respectively. These markers are thus suitable candidates for marker assisted selection in groundnut. The tight linkage of SSR_GO340445 would be helpful to screen BAC clones and to isolate rust resistance gene in groundnut.     

花生EST-SSR分子标记的开发

利用NCBI的Genbank数据库中公布的花生53177条EST序列以及本实验室创造的花生栽培品种E12(Arachis hypogaea L.)所构建的Unigene文库中的4 074条EST序列,对这些序列进行前期处理(去除冗余序列,对含有重叠区域的EST序列进行拼接),总共获得非冗余且拼接较长的序列11 260条.通过软件分析发现两个EST库中共包含有1 323个SSR位点,主要是2个和3个核苷酸重复,除此之外也有少量的4核苷酸重复以及复合重复.这些EST-SSR平均长度为18.88 bp,平均每8.5条EST序列就包含有一个SSR位点.其中AG/TC、CTY/GAA重复出现的频率最大,分别占到2个核苷酸重复和3个核苷酸重复的39.3%和22.6%.     

Evaluation of components of field resistance to the Pythium pod rot complex in groundnut (Arachis hypogaea L.) cultivars

Summary The disease indices of homogenous populations, as compiled from field data, measure field resistance. Since the disease level in a population is the product of disease severity in diseased plants and their frequency, it may be illustrated by a rectangle. This presentation facilitates analysis of the contribution, to field resistance, of tissue resistance versus escape ability.Contribution from The Volcani Center, Agricultural Research Organization, Bet Dagan, Israel. 1972 Series, No 2211-E.     

SSR markers associated for late leaf spot disease resistance by bulked segregant analysis in groundnut (Arachis hypogaea L.)

Late leaf spot (LLS) caused by Phaeoisariopsis personata is the major foliar disease that reduces the pod yield and severely affects the fodder and seed quality in groundnut. Molecular markers linked with LLS can improve the process of identification of resistant genotypes. In the present study, a LLS susceptible genotype (TMV 2) and the LLS resistant genotype (COG 0437) were crossed and their F₂ population was used for marker analysis. The phenotypic mean data on F_2:3 progenies were used as phenotype. Parents were surveyed with 77 SSR (Simple Sequence Repeat) primers to identify polymorphic markers. Among SSR markers, nine primers were found polymorphic between the parents TMV 2 and COG 0437. These markers were utilized for bulked segregant analysis (BSA). Among the polymorphic SSR markers, three primers viz., PM 375₁₆₂, pPGPseq5D5₂₂₀ and PM 384₁₀₀ were able to distinguish the resistant and susceptible bulks and individuals for LLS. In single marker analysis, the markers PM 375, PM 384, pPGPseq5D5, PM 137, PM 3, PMc 588 and Ah 4-26 were linked with LLS severity score. The phenotypic variation explained by these markers ranged from 32 to 59?%. The markers identified through BSA were also confirmed with single marker analysis. While validating the three primers over a set of resistant and susceptible genotypes, the primer PM 384₁₀₀ allele had association with resistance. Hence PM 384 could be utilized in the marker assisted breeding programme over a wide range of genetic background.     

High level of natural variation in a groundnut (Arachis hypogaea L.) germplasm collection assayed by selected informative SSR markers

The ability to identify genetic variation is indispensable for effective management and use of genetic resources in crop breeding. Genetic variation among 189 groundnut ( Arachis hypogaea L.) accessions comprising landraces, cultivars, a mutant, advanced breeding lines and others (unknown genetic background) representing 29 countries and 10 geographical regions was assessed at 25 microsatellite or simple sequence repeat loci. A high number of alleles (265) were detected in the range of 3 (Ah1TC6G09) to 20 (Ah1TC11H06) with an average of 10.6 alleles per locus. The polymorphism information content value at these loci varied from 0.38 (Ah1TC6G09) to 0.88 (Ah1TC11H06) with an average of 0.70. A total of 59 unique alleles and 127 rare alleles were detected at almost all the loci assayed. Cluster analysis grouped 189 accessions into four clusters. In general, genotypes of South America and South Asia showed high level of diversity. Extraordinary level of natural genetic variation reported here provides opportunities to the groundnut community to make better decisions and define suitable strategies for harnessing the genetic variation in groundnut breeding.     

花生栽培种EST-SSRs分布特征及应用研究

利用自行开发的20 160条花生栽培种荚果EST, 通过序列拼接, 获得8 289条无冗余EST。经搜索, 共检测出740个SSR位点, 分布于651条EST中, 发生频率为7.8%, 平均每6.8 kb EST序列含一个SSR位点。功能注释结果表明具生物过程、分子功能和细胞组分的EST分别为73、111和56条。在花生荚果EST-SSR中, 三核苷酸重复类型出现频率最高, 占总SSR的62.8%, 其次是二核苷酸重复类型, 占总SSR的33.6%。在出现的26类重复基序中, AG/TC重复基序出现频率最高, AAG/TTC次之。利用Primer premier 5从651条含有SSR的EST中共设计引物233对, 从中随机选取100对引物检测EST-SSR在花生栽培种中的多态性及在野生种中的可转移性。结果表明, 有86对引物在供试的22个花生栽培品种中得到有效扩增, 其中10对在栽培种中具有多态性, 每对引物检测出的等位基因数2~3个, 平均2.2个。可扩增引物在野生种中的可转移率为12.5%~100%,平均96%。在野生种间检测出多态性的引物76对,每对引物检测出等位基因2~9个, 平均4.06个。