Biparental Crosses Research Articles

Combining ability of popcorn lines for seed quality and agronomic traits

Popcorn breeding programs in Brazil have emerged but despite some advances there is still a lack of material performance studies specially regard to seed quality, in different agricultural seasons. This research was carried out to estimate the popcorn combining ability from biparental crosses between eight tropical and one temperate lines in two agricultural seasons (2008 and 2009) with regard to eight traits related to seed quality, in addition to three agronomic traits related to popping expansion. Method 4, proposed by Griffing (Model 1), was used to verifying the importance of the dominance effect in the genetic control of the seed quality traits, favouring the identification of superior hybrids through seed tests in the laboratory with low cost. The lines from Zelia and CMS42 were promising in obtaining hybrids with superior seed quality and greater popping expansion. The hybrids Zelia × IAC-112, CMS42 × UEM M2-1, CMS43-1 × IAC-112 and UEM M2-2 × Zaeli expressed superior SCA for grain yield, popping expansion and at least two seed quality traits. These hybrids are materials of interest for cultivation in different planting seasons.

R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines

Multiparent crosses of recombinant inbred lines provide opportunity to map markers and quantitative trait loci (QTL) with much greater resolution than is possible in biparental crosses. Realizing the full potential of these crosses requires computational tools capable of handling the increased statistical complexity of the analyses. R/mpMap provides a flexible and extensible environment, which interfaces easily with other packages to satisfy this demand. Functions in the package encompass simulation, marker map construction, haplotype reconstruction and QTL mapping. We demonstrate the easy-to-use features of mpMap through a simulated data example. www.cmis.csiro.au/mpMap.

Association mapping for phenological, morphological, and quality traits in canola quality winter rapeseed (Brassica napusL.)This article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

QTL mapping by association analysis has recently gained interest in plant breeding research as an alternative to QTL mapping in segregating populations from biparental crosses. In a first experiment on whole-genome association analysis in rapeseed, 684 mapped AFLP markers were tested for association with 14 traits in a set of 84 canola quality winter rapeseed cultivars. For association analysis a general linear model was used. By testing significance of marker-trait associations against a false discovery rate of 0.2, between 1 and 34 associated markers were found for 10 of the 14 traits. Taking into account linkage disequilibrium between the significant markers, these markers represent between 1 and 22 putative QTL for the respective traits. The minimum phenotypic variance explained by the QTL for the different traits ranged from 15% to 53%. A subset of 27 markers were significantly associated with two or more traits. These markers were predominantly shared between traits that were significantly correlated at the phenotypic level. The results show clearly that in rapeseed, QTL mapping by association analysis is a viable alternative to QTL mapping in segregating populations.

Comparison of biparental and melting pot methods of crossing sugarcane in Hawaii

Sugarcane (Saccharum hybrid spp.) breeders at the Hawaiian Sugar Planters’ Association used biparental and melting pot (modified polycross) crossing methods concurrently from 1935 to 1985. While the annual effort expended to make biparental crosses exceeded the effort to make melting pot crosses over this 50-year period, annual viable seed yield from biparental crosses was usually less than 15% of that from melting pot crosses and hence, the numbers of seedlings planted to the field from those crosses usually accounted for less than 20% of the total seedling population. In 1985, nine of the 10 sugarcane cultivars listed in Hawaii’s variety census originated from melting pot crosses; only one originated from a biparental cross. In the face of a shrinking sugar industry in Hawaii and a smaller work force in the breeding program, the decision was made in 1985 to rely primarily on melting pot crosses for the production of commercial cultivars. From 1985 to 2005, twelve additional clones that were bred prior to 1985 eventually attained “commercial cultivar” status by exceeding 1% of the total cane growing area. All twelve originated from melting pot crosses. Over the 50-year period that the two crossing methods were used, the melting pot method proved to be more labour efficient and ultimately contributed more than the biparental crossing procedure toward the development of new commercial cultivars for the Hawaiian sugar industry. From 1985 forward, the biparental crossing method was used more for introgressing desired traits from exotic germplasm than for the development of commercial cultivars.

Physical purity and germination of sugarcane seeds (caryopses) (Saccharum spp.)

Plant breeding is generally done through sexual reproduction even when the species is propagated asexually for commercial exploitation, as for example, in sugarcane. Therefore, the development of procedures to evaluate sugarcane seed viability is important for plant breeding programs. The objective of this research was to develop a methodology for analyzing the viability of sugarcane seeds (Saccharum spp.). Three crosses were used, two biparental crosses and one polycross. For the germination test study, two substrates (paper and sand) and three constant incubation temperatures (25 ºC, 30 ºC and 35 ºC), in the presence of constant light and also an alternating temperatures (20-30 ºC), with 8 hours light (30 ºC) and 16 hours darkness (20 ºC), were studied. Seedlings were evaluated every five days. The results demonstrated that temperature affected sugarcane seed germination with the most favorable conditions being the alternating temperature (20-30 ºC) and the constant temperature of 30 ºC on a paper substrate.

Genetic map-based location of the red clover (Trifolium pratense L.) gametophytic self-incompatibility locus

Red clover is a hermaphroditic allogamous diploid (2n = 2x = 14) with a homomorphic gametophytic self-incompatibility (GSI) system (Trifolium pratense L.). Red clover GSI has long been studied, and it is thought that the genetic control of GSI constitutes a single locus. Although GSI genes have been identified in other species, the genomic location of the red clover GSI-locus remains unknown. The objective of this study was to use a mapping-based approach to identify simple sequence repeats (SSR) that were closely linked to the GSI-locus. Previously published SSR markers were used in this effort (Sato et al. in DNA Res 12:301-364, 2005). A bi-parental cross was initiated in which the parents were known to have one self-incompatibility allele (S-allele) in common. S-allele genotypes of 100 progeny were determined through test crosses and pollen compatibility. Pseudo F(1) linkage analysis isolated the GSI-locus on red clover linkage-group one within 2.5 cM of markers RCS5615, RCS0810, and RCS3161. A second 256 progeny mapping testcross population of a heterozygous self-compatible mutant revealed that this specific self-compatible mutant mapped to the same location as the GSI-locus. Finally, 82 genotypes were identified whose parents putatively shared one S-allele in common from maternal halfsib families derived from two random mating populations in which paternal identity was determined using molecular markers. Unique S-allele identity in the two random mating populations was tentatively inferred based on haplotypes of two highly allelic linkage-group one SSR (RCS0810 and RCS4956), which were closely linked to each other and the GSI-locus. Paternally derived pollen haplotype linkage analysis of RCS0810 and RCS4956 SSR and the GSI-locus again revealed tight linkage at 2.5 and 4.7 cM between the GSI-locus and RCS0810 and RCS4956, respectively. The map-based location of the GSI-locus in red clover has many immediate applications to red clover plant breeding and could be useful in helping to sequence the GSI-locus.

A preliminary genetic linkage map of chrysanthemum ( Chrysanthemum morifolium) cultivars using RAPD, ISSR and AFLP markers

A genetic linkage map of chrysanthemum ( Chrysanthemum morifolium) was constructed by genotyping 142 F 1 progeny of the bi-parental cross ‘Yuhualuoying’ × ‘Aoyunhanxiao’ with a combination of RAPD, ISSR and AFLP markers in a double pseudo-testcross mapping strategy. A total of 567 polymorphic markers, including 153 RAPDs, 61 ISSRs and 353 AFLPs, were used in linkage mapping. 336 of 567 (60%) markers were grouped on the two parental maps, leaving 231 (40%) markers unlinked. In the ‘Yuhualuoying’ linkage map, 210 markers including 116 testcross and 94 intercross markers were placed in 12 major and 32 minor (8 triplets and 24 doublets) linkage groups, covering 1034 cM with an average map distance of 6.2 cM between adjacent markers. In ‘Aoyunhanxiao’ linkage map, 190 markers consisting of 113 testcross and 77 intercross markers were resolved into 9 major and 24 minor linkage groups, with genome coverage of 1095 cM and a mean inter-marker separation of 6.9 cM between adjacent markers. Six pairs of homologous linkage groups were established on the basis of 64 intercross markers shared by the two parental maps. The maps lay a foundation for further quantitative traits loci (QTL) mapping and marker-assisted breeding of chrysanthemum.

Variation of the parental genome contribution in segregating populations derived from biparental crosses and its relationship with heterosis of their Design III progenies

The variation of the parental genome contribution (PGC) and its relationship with the genetic architecture of heterosis have received little attention. Our objectives were to (1) derive formulas for the variance of PGC in selfing, backcross (BC) or intermated generations produced from biparental crosses of homozygous parents, (2) investigate the correlation [Formula: see text] of the PGC [Formula: see text] estimated by a set M of markers, with Z (2) (half the trait difference between each pair of BC progenies) in the Design III, and (3) interpret experimental results on this correlation with regard to the genetic basis of heterosis. Under all mating systems, the variance of PGC is smaller in species with a larger number and more uniform length of chromosomes. It decreases with intermating and backcrossing but increases under selfing. The ratio of variances of PGC in F(1)DH (double haploids), F(2) and BC(1) populations is 4:2:1, but it is smaller in advanced selfing generations than expected for quantitative traits. Thus, altering the PGC by marker-assisted selection for the genetic background is more promising (i) in species with a smaller number and/or shorter chromosomes and (ii) in F(2) than in progenies of later selfing generations. The correlation [Formula: see text] depends on the linkage relationships between M and the QTL influencing Z(2) as well as the augmented dominance effects [Formula: see text] of the QTL, which include dominance and additive x additive effects with the genetic background, and sum up to mid-parent heterosis. From estimates of [Formula: see text] as well as QTL studies, we conclude that heterosis for grain yield in maize is caused by the action of numerous QTL distributed across the entire genome with positive [Formula: see text] effects.

Analysis of genomic and functional RFLP derived markers associated with sucrose content, fiber and yield QTLs in a sugarcane (Saccharum spp.) commercial cross

Expressed sequence tags derived markers have a great potential to be used in functional map construction and QTL tagging. In the present work, sugarcane genomic probes and expressed sequence tags having homology to genes, mostly involved in carbohydrate metabolism were used in RFLP assays to identify putative QTLs as well as their epistatic interactions for fiber content, cane yield, pol and tones of sugar per hectare, at two crop cycles in a progeny derived from a bi-parental cross of sugarcane elite materials. A hundred and twenty marker trait associations were found, of which 26 at both crop cycle and 32 only at first ratoon cane. A sucrose synthase derived marker was associated with a putative QTL having a high negative effect on cane yield and also with a QTL having a positive effect on Pol at both crop cycles. Fifty digenic epistatic marker interactions were identified for the four traits evaluated. Of these, only two were observed at both crop cycles.

Seleção de linhagens experimentais de soja para características agronômicas e tolerância a insetos

Esta pesquisa visou avaliar linhagens experimentais de soja, com a finalidade de identificar genótipos que reúnam características de alta produtividade e tolerância a insetos. O material foi composto por três populações obtidas de um dialelo parcial 4 x 4 envolvendo quatro genitores tolerantes a insetos e quatro cultivares de elevada produtividade. Foram conduzidos 24 experimentos no delineamento aleatório, em blocos com duas repetições subdivididas em conjuntos experimentais com testemunhas comuns, combinando as três populações e oito ambientes. Com base na produtividade de grãos, concluiu-se que: existe variabilidade genética remanescente entre as linhagens nas três populações; o manejo diferenciado com controle intensivo de insetos e controle ecológico de insetos (CII vs. CEI) é um representante eficiente de ambientes diversos; o local Anhembi destacou-se como de alta produtividade em todas as situações; para a capacidade de gerar linhagens superiores, sobressaíram-se os genitores IAC-100, D72-9601-1, BR-6, Davis e IAS-5; destaques especiais envolveram os cruzamentos do genitor IAC-100 com IAS-5, Davis, OCEPAR-4 e BR-6.

Registration of Six Tropical Maize Germplasm Lines with Resistance to Aflatoxin Contamination

Six tropical maize (Zea mays L.) germplasm lines, TZAR101 (Reg. No. GP‐568, PI 654048), TZAR102 (Reg. No. GP‐569, PI 654049), TZAR103 (Reg. No. GP‐570, PI 654050), TZAR104 (Reg. No. GP‐571, PI 654051), TZAR105 (Reg. No. GP‐572, PI 654052), and TZAR106 (Reg. No. GP‐573, PI 654053), with resistance to aflatoxin contamination were developed by the International Institute of Tropical Agriculture through a collaborative breeding project with Southern Regional Research Center of the USDA‐ARS. The lines were derived from biparental crosses and backcross populations involving aflatoxin‐resistant tropical elite and temperate inbred lines as parents. These lines had aflatoxin levels similar to or lower than a resistant U.S. inbred check, MI82, in both preliminary and confirmation tests conducted in the laboratory using a kernel‐based screening assay. Further field tests of the six lines under artificial inoculation with an African strain of Aspergillus flavus in Nigeria revealed that these lines had lower levels of aflatoxin compared with elite tropical commercial inbred lines used as checks. These lines also had good agronomic traits and resistance to important diseases in the lowlands, including southern corn leaf blight [caused by Bipolaris maydis (Nisikado & Miyake) Shoemaker], southern corn rust (caused by Puccinia polysora Underw.), and ear rot.

A RE-INTERPRETATION OF HYBRID VIGOUR IN COCOA

SUMMARYFor 50 years, ‘hybrid vigour’ in crosses involving genotypes collected from the centre of diversity of the crop in the Peruvian Amazon has been the guiding principle of cocoa breeding. In the work described here, six Amazonian genotypes and one Trinitario clone were used to produce four bi-parental crosses. Twenty-two plants of each cross were propagated from plagiotropic buds as ‘cloned seedlings’ and evaluated for growth, yield and yield efficiency (the ratio of yield to continuing vegetative growth) in replicated trials in comparison with the parental clones and the reproduced seedling family. The reproduced seedling families grew faster than and outyielded all the clones in all four crosses, although they showed no gain in yield efficiency. The vigour and yield of the ‘cloned seedlings’ of the three inter-Amazon crosses exceeded mid-parent value (MPV), but not the single Trinitario cross. The pattern of departures from MPVs was inconsistent with current understanding of the genetic distance between the parents. The superiority of the seedlings over the ‘cloned seedlings’ is interpreted as an epigenetic effect. The results suggest that simple recurrent selection is an appropriate breeding strategy in cocoa, with different optimum planting densities for the seedling and clonal phases. It is concluded that if the concept of very large ‘hybrid vigour’ did not already exist in cocoa, it would not be adopted on the evidence of this work, the first in which clones were compared to their progeny grown as clones.

SELEÇÃO DE FAMÍLIAS DE CANA-DE-AÇÚCAR VIA MODELOS MISTOS

O objetivo deste trabalho, selecionar famílias superiores de cana-de-açúcar oriundas de cruzamentos biparentais, para produção de biomassa via modelos mistos. Adotou-se a metodologia REML/BLUP, onde o REML permitiu estimar a variância genética e o BLUP a estimar os valores genéticos das famílias utilizadas no presente estudo. Foram utilizadas 80 famílias originadas de cruzamentos biparentais da série RB03, provenientes de cruzamentos realizados na Estação de Cruzamentos Serra do Ouro, Município de Murici, Alagoas, no ano de 2003. O trabalho foi conduzido em área experimental, localizada no Município de São Tomé, Paraná. O delineamento estatístico do experimento foi em blocos incompletos, com cinco repetições por família. Cada parcela foi composta de dez plantas. Para seleção das famílias superiores adotou-se a produção de biomassa expressa em tonelada de cana por hectare (TCH). De acordo com os resultados obtidos, verificou-se que a herdabilidade individual () apresentou média magnitude (0,22), enquanto que em nível de famílias a herdabilidade média das famílias () foi alta magnitude (0,73). Ao realizar a seleção das famílias com valores genotípicos acima da média experimental, estima-se ganhos significativos para TCH. Sendo que as cinco melhores famílias para TCH foram originadas dos cruzamentos biparentais RB825336 e SP80-1816, RB825548 e RB855156, SP80-3280 e RB845257, RB83102 e RB855113, RB8495 e RB835089.

Evaluation of Sugarcane × Saccharum spontaneum Progeny for Biomass Composition and Yield Components

Saccharum spontaneum L. has contributed important traits to modern sugarcane (S. spp. L.) cultivars such as adaptation to environmental stress and ratooning ability. There is interest in further use of S. spontaneum in sugarcane improvement for sugar or energy‐from‐biomass production systems. In this study, parents and progeny from 43 biparental crosses between sugarcane and S. spontaneum clones were evaluated in field trials in China and Australia, along with several commercial cultivars. The S. spontaneum clones were from diverse geographic origins in China. Measurements were made on biomass composition (% dry matter, brix and pol in juice and cane, purity, fiber content) and yield components. Moderate to high (>0.7) broad‐sense heritabilities and high genetic variances were observed for most traits. About half the total genetic variance was retained as among‐family variance for the biomass composition traits, but this proportion was generally <25% for biomass yields. Midparent values in an independent trial predicted biomass composition traits reasonably well (generally, r > 0.6), but less so for cane and biomass yield (0 < r < 0.4). Genetic correlations between performance of families evaluated in different countries were strong, providing preliminary evidence that results in one country could be used for identifying elite families in the other. Strategies for efficient development and selection of elite clones from S. spontaneum are suggested.

New soybean (Glycine max Fabales, Fabaceae) sources of qualitative genetic resistance to Asian soybean rust caused by Phakopsora pachyrhizi (Uredinales, Phakopsoraceae)

Asian soybean rust (ASR), caused by the phytopathogenic fungi Phakopsora pachyrhizi, has caused large reductions in soybean (Glycine max) yield in most locations in Brazil where it has occurred since it was first reported in May 2001. Primary efforts to combat the disease involve the development of resistant cultivars, and four dominant major genes (Rpp1, Rpp2, Rpp3 and Rpp4) controlling resistance to ASR have been reported in the literature. To develop new long-lasting soybean ASR resistance genes, we used field experiments to assess ASR leaf lesion type in 11 soybean genotypes (BR01-18437, BRS 184, BRS 231, BRS 232, BRSGO Chapadões, DM 339, Embrapa 48, PI 200487, PI 230970, PI 459025-A and PI 200526) and the 55 F2 generations derived from their biparental diallel crosses. The results indicated that PI 200487 and PI 200526 carry different dominant resistance major genes which are both different from Rpp2 through Rpp4. Furthermore, resistance to ASR in BR01-18437 is controlled by a single recessive major gene, also different from Rpp1 through Rpp4 and different from the genes in PI 200487 and PI 200526.

The inheritance of systemic resistance to the bacterial blight pathogen ( Xanthomonas axonopodis pv. dieffenbachiae) in Anthurium andraeanum (Hort.)

The inheritance of resistance to systemic infection by bacterial blight disease (blight) caused by Xanthomonas axonopodis pv. dieffenbachiae in anthurium ( Anthurium andraeanum Hort.) was investigated in 83 biparental crosses involving 39 anthurium cultivars, using a green fluorescent protein-based screening method. Genetic analysis was based on North Carolina mating design II analysis, combining ability analysis and parent–offspring regression analysis. The results showed a role for both additive and non-additive effects in the inheritance of systemic resistance to blight, although the former was predominant and between four- to five-fold larger than the latter. General combining ability (GCA) of the parents was able to fairly accurately predict the performance of progeny in 15 of the 17 M × N (‘M’ male cultivars crossed with ‘N’ female cultivars) mating designs. The highly resistant cultivars were the best general combiners, while the susceptible cultivars generally produced negative GCA values. Dominance was in the direction of susceptibility. Narrow sense heritability ( h 2) based on North Carolina mating design II analysis, was 42.5%, with broad sense heritability ( H 2) of 96.5%. The estimate of h 2 based on mid-parent–offspring regression analysis was slightly higher (58–62%). In conclusion, the results indicated that resistance to systemic blight is governed by both additive and non-additive genetic effects with the former playing a larger role. Clonal breeding for systemic resistance to blight using a family selection approach is suggested.

Genetic Diversity in Cocoa (Theobroma cacao L.) Germplasm Collection from Ghana

Theobroma cacao L. with its center of diversity in Central and South America was first introduced to West Africa in the mid-19th century and today the region produces 70% of the world's cocoa. Several distinct cocoa types have been introduced, cultivated, and intercrossed across the region. Also, bi-parental crosses involving selections from various introductions have been planted on a large scale. Consequently, a wide range of genetic diversity that could be exploited for crop improvement is expected. The present study has been, therefore, undertaken to assess the degree and distribution of genetic diversity present in cocoa germplasm collections from the Cocoa Research Institute (CRIG), seed gardens and materials from farmers' plantations in Ghana, using molecular markers. Two hundred and thirty-five trees representing all the cocoa-growing regions of Ghana were sampled in situ from farmers' fields and grouped as farmers' collection. Another set of 104 trees was collected from breeders' seed gardens, called breeders' collection. Thirty-eight parental clones from the CRIG's collection, used in producing the bi-parental crosses, comprised the third category, called parental clones. The collections were screened with the set of 17 mapped microsatellite markers. Average gene diversity was high in all populations, with mean observed heterozygosity of 0.738. Although the highest was recorded in accessions from breeders' and parental collections, genetic diversity in the farmers' collection was comparable with them. Despite the low level of differentiation [Fst = 0.076] found across all the three groups, sufficient genetic differences existed between them, separating breeders' collection from farmers' collection. The study also revealed the pattern of adoption of available planting materials by farmers on their fields.

Identification for tolerance to fruit set in tomato by fAFLP markers

This study aimed to detect quantitative trait loci (QTL) by fAFLP (Fluorescent Amplified Fragment Length Polymorphism) markers associated to the trait tomato fruit set at high temperatures. A biparental cross between line Jab-95 (heat-tolerant) and cultivar Caribe (heat-susceptible) was made. A total of 192 plants of the F2 generation were evaluated, generating 172 polymorphic markers through six primer combinations previously identified by the Bulked Segregant Analysis technique. To constr uct the genetic map, 106 of the 172 markers that segregated in the expected Mendelian segregation proportion (3:1) were used. The map covered 1191.46 cM of the genome. Six trait-linked QTL were identified in the analysis of simple markers and three others by the interval-mapping methodology. These results could be highly useful in improvement programs, since heat-tolerant plants can be selected rapidly, which improves tomato fruit set.

Variance of the Parental Genome Contribution to Inbred Lines Derived From Biparental Crosses

The expectation of the parental genome contribution to inbred lines derived from biparental crosses or backcrosses is well known, but no theoretical results exist for its variance. Our objective was to derive the variance of the parental genome contribution to inbred lines developed by the single-seed descent or double haploid method from biparental crosses or backcrosses. We derived formulas and tabulated results for the variance of the parental genome contribution depending on the chromosome lengths and the mating scheme used for inbred line development. A normal approximation of the probability distribution function of the parental genome contribution fitted well the exact distribution obtained from computer simulations. We determined upper and lower quantiles of the parental genome contribution for model genomes of sugar beet, maize, and wheat using normal approximations. These can be employed to detect essentially derived varieties in the context of plant variety protection. Furthermore, we outlined the application of our results to predict the response to selection. Our results on the variance of the parental genome contribution can assist breeders and geneticists in the design of experiments or breeding programs by assessing the variation around the mean parental genome contribution for alternative crossing schemes.

A Modified Algorithm for the Improvement of Composite Interval Mapping

Composite interval mapping (CIM) is the most commonly used method for mapping quantitative trait loci (QTL) with populations derived from biparental crosses. However, the algorithm implemented in the popular QTL Cartographer software may not completely ensure all its advantageous properties. In addition, different background marker selection methods may give very different mapping results, and the nature of the preferred method is not clear. A modified algorithm called inclusive composite interval mapping (ICIM) is proposed in this article. In ICIM, marker selection is conducted only once through stepwise regression by considering all marker information simultaneously, and the phenotypic values are then adjusted by all markers retained in the regression equation except the two markers flanking the current mapping interval. The adjusted phenotypic values are finally used in interval mapping (IM). The modified algorithm has a simpler form than that used in CIM, but a faster convergence speed. ICIM retains all advantages of CIM over IM and avoids the possible increase of sampling variance and the complicated background marker selection process in CIM. Extensive simulations using two genomes and various genetic models indicated that ICIM has increased detection power, a reduced false detection rate, and less biased estimates of QTL effects.