Pyramiding three rust‐resistance genes confers a high level of resistance in soybean (Glycine max)

Pyramiding Asian soybean rust (ASR) resistance (Rpp) genes in a single genotype has been shown to increase ASR resistance in soybean. However, it remains unclear which combinations of Rpp genes are superior. Therefore, here, we developed six new Rpp‐pyramided lines carrying different combinations of Rpp genes and evaluated their resistance against 13 Bangladeshi rust (Phakopsora pachyrhizi) isolates (BdRPs) alongside seven previously developed Rpp‐pyramided lines. We found that lines carrying one, two and three Rpp genes had high ASR resistance without sporulation in 13.8%, 35.2% and 73.1% of the assays, respectively. Among the new lines that were developed, those with Rpp3 + Rpp4 and Rpp3 + Rpp4 + Rpp5 had high levels of ASR resistance, while the line containing Rpp2 + Rpp4 + Rpp5 showed immunity phenotype at two weeks after inoculation by the BdRP‐22 infection. Thus, pyramiding larger numbers of Rpp genes confers soybean with a higher level of resistance to ASR pathogens and can produce an immunity phenotype at two weeks after inoculation.     

The locus for resistance to Asian soybean rust in PI 587855

Asian soybean rust (ASR) caused by Phakopsora pachyrhizi is one of the most serious soybean (Glycine max) diseases in tropical and subtropical areas. A soybean line, PI 587855, showed a resistance phenotype against ASR pathogens in Japan and South America at high frequency; however, little is known of the genetic control of this resistance and chromosomal location of the corresponding locus. Therefore, the aim of this study was to study the inheritance of PI 587855 resistance and map the corresponding locus with SSR markers aiming to use the linked markers in marker‐assisted selection. In the segregating population, resistance to ASR appeared to be controlled by a single dominant gene. The ASR resistance locus was mapped near to the chromosomal region where the resistant loci, Rpp1 and Rpp1‐b, were previously mapped. Comparative genetic mapping and disease reaction profiles of other seven lines carrying Rpp1 or Rpp1‐b to four Brazilian ASR isolates revealed that the resistance reaction exhibited by PI 587855 was similar to that of Rpp1‐b‐carrying varieties which have useful resistance to South American ASR strains.     

Inheritance and mapping of resistance against Cowpea mild mottle virus strain D1 in soybean

Cowpea mild mottle virus (CPMMV) is an emerging severe disease of soybean. The resistant genotypes, DS 12‐5 and SL958, were crossed with susceptible genotypes F4C7‐32 and JS335, respectively. Resistance reactions of sap‐inoculated F₂ plants and individual F₂ plant‐derived F₃ families indicated that resistance was controlled by a single dominant gene. Molecular mapping with bulked segregant analysis showed that Satt635 and UO8405 are linked to resistance gene which is located on linkage group H.     

Identification and validation of an over‐dominant QTL controlling soybean seed weight using populations derived from Glycine max × Glycine soja

Heterosis, or hybrid vigour, has been used to improve seed yield in several important crops for decades and it has potential applications in soybean. The discovery of over‐dominant quantitative trait loci (QTL) underlying yield‐related traits, such as seed weight, will facilitate hybrid soybean breeding via marker‐assisted selection. In this study, F₂ and F_2 : 3 populations derived from the crosses of ‘Jidou 12’ (Glycine max) × ‘ZYD2738’ (Glycine soja) and ‘Jidou 9’ (G. max) × ‘ZYD2738’ were used to identify over‐dominant QTL associated with seed weight. A total of seven QTL were identified. Among them, qSWT_13_1, mapped on chromosome 13 and linked with Satt114, showed an over‐dominant effect in two populations for two successive generations. This over‐dominant effect was further examined by six subpopulations derived from ‘Jidou12’ × ‘ZYD2738’. The seed weight for heterozygous individuals was 1.1‐ to 1.6‐fold higher than that of homozygous individuals among the six validation populations examined in different locations and years. Therefore, qSWT_13_1 may be a useful locus to improve the yield of hybrid soybean and to understand the molecular mechanism of heterosis in soybean.     

The transition time from the juvenile phase to the adult phase differs in soybean cultivars ‘Enrei’ and ‘Peking’

Plants develop juvenile phase to adult phase in vegetative stage. Although soybean is a very important crop worldwide, there has been only one study of the juvenile–adult phase change. In this study, we determined that the juvenile–adult phase change occurred at different stages in two soybean cultivars that differ in their photosensitivity. Cultivar ‘Enrei’ (E1e2e3E4) is weakly photosensitive and cultivar ‘Peking’ (E1E2E3E4) is strongly photosensitive. In ‘Enrei’, the leaf size gradually increased at a constant leaf position regardless of the difference in day length. In ‘Peking’ plants transferred to short‐day conditions at several leaf development stages, leaf size gradually increased at different leaf positions. Expression of miR156 by ‘Enrei’ transferred to short‐day conditions had nearly the same pattern as that of ‘Enrei’ grown under long‐day conditions. In ‘Peking’, the expression of miR156 had different patterns in younger leaves of plants subjected to either a short‐day treatment or long‐day conditions. These results indicate that the E2 and E3 loci that regulate photosensitivity also regulate the expression of miR156 and the juvenile–adult phase change in soybean.     

Breeding and characterization of soybean Triple Null; a stack of recessive alleles of Kunitz Trypsin Inhibitor,Soybean Agglutinin,and P34 allergen nulls

Soybean (Glycine max) seeds contain bioactive proteins with antinutritional and immunological properties that affect metabolism and assimilation of nutrients. The presence of antinutritional proteins requires soybeans to be heat‐treated resulting in input energy costs. Nulls for bioactive seed proteins have been previously isolated from the USDA soybean collection, including Kunitz trypsin inhibitor (TI), soybean agglutinin (LE) and immunodominant soybean allergen P34 protein. Each of these nulls has the potential to partially address the concerns of soybean feed/food consumption. A stack of recessive nulls of TI, LE and P34 was created in a cv ‘Williams 82’ background termed ‘Triple Null’. Triple Null has a slight reduction of total protein compared with ‘Williams 82’ corresponding to aggregate contribution of TI, LE and P34 in the seed proteome. Triple Null's proteome analysis revealed P34 and TI nulls are frame‐shift mutants able to accumulate small amounts of authentic P34 and TI proteins. Triple Null has possible application as a conventional feed/food source and for immunotherapy to mitigate soybean allergenic response.     

Methodology for creating alloplasmic soybean lines by using Glycine tomentella as a maternal parent

Soybean breeders have not exploited the diversity of the 26 wild perennial species of the subgenus Glycine Willd. that are distantly related to soybean [Glycine max (L.) Merr.] and harbour useful genes. The objective of this study was to develop a methodology for introgressing cytoplasmic and genetic diversity from Glycine tomentella PI 441001 (2n = 78) into cultivated soybean using ‘Dwight’ (2n = 40) as the male parent. Immature seeds (19–21 days post‐pollination) were cultured in vitro to produce F₁ plants (2n = 59). Amphidiploid (2n = 118) plants, induced by colchicine treatment, were vigorous and produced mature pods and seeds after backcrossing with ‘Dwight’. The BC₁ plants (2n = 79) produced mature seeds in crosses with ‘Dwight’. Chromosome numbers in BC₂F₁ plants ranged from 2n = 41–50. From BC₂F₂ to BC₃F₁, the number of plants in parentheses with 2n = 40 (275), 2n = 41 (208), 2n = 42 (80), 2n = 43 (27), 2n = 44 (12) and 2n = 45 (3) were identified. Fertile lines were grown in the field during 2012 and 2013. This is the first report of the successful development of new alloplasmic soybean lines with cytoplasm from G. tomentella.     

Independent selection for seed free tryptophan content and vernalization response in chickpea domestication

Chickpea shows a distinct domestication trajectory vis‐a‐vis pod dehiscence and growth cycle mediated by vernalization insensitivity compared with its companion Near Eastern legumes. Our objectives were: (i) to map the quantitative trait loci (QTLs) associated with vernalization response and seed free tryptophan in domesticated × wild chickpea progeny and (ii) estimate the genetic correlation between vernalization response and free tryptophan content. A domesticated × wild chickpea cross was used to document phenotypic segregation in both traits and to construct a skeletal genetic map for QTL detection. A number of vernalization response and seed free tryptophan content QTLs were documented in both F₂ and F₃ generations. No significant genetic correlation between these two traits was observed. Epistatic relationship between two free tryptophan loci was documented. It is evident that selection for high seed tryptophan is easier to accomplish relative to selection for vernalization insensitivity. This suggests that the two traits were selected independently in antiquity, thereby corroborating earlier claims for conscious selection processes associated with chickpea domestication.     

Inheritance of the four-seeded-pod trait in a soybean mutant and marker-assisted selection for this trait

A high seeds‐per‐pod value is a crucial component of soybean seed yield, but reliable information is lacking on the inheritance and early selection for the four‐seeded pod (4SP) trait. The inheritance of 4SP was followed in crosses originating from an EMS‐derived mutant line (E182, 15% 4SP) with its parental cultivar, ‘Ludou No. 4’ (no 4SP), and the efficiencies of both a molecular and morphological marker selection were determined. The plants of two F₂ populations (with E182 as one of the parents) showed a segregation ratio of 3 : 1 (low to high SP values), indicating a single recessive locus; this mode of inheritance was confirmed by subsequent analysis of the F_{2 : 3} families. Among four microsatellite markers linked with the 4SP trait, Sat_107 was the closest to the 4SP locus (3.2 ± 1.11 cM). Both the molecular marker Sat_107 and the morphological marker, narrow leaflet (NL) associated with the 4SP locus were effective in selecting the 4SP trait, although with different efficiencies. The molecular marker was efficient in selecting soybean progenies from the cross in which one parent was the E182 mutant line because it was tightly linked to the mutated 4SP locus. In the other cross, with 4SP not derived from E182, the efficiency was reduced in comparison with the morphological marker.     

Maternal inheritance of male sterility in the progeny of a natural hybrid between Cajanus lineatus and C. cajan

Adoption of pigeonpea hybrids in central and southern India is showing high impact with on‐farm yield advantages of >30%. The hybrid pigeonpea technology, the first in any legume crop, is based on a cytoplasmic‐nuclear male‐sterility (CMS) system. For a long‐term sustainability of hybrid programme, it is imperative that both nuclear diversity and cytoplasmic diversity are maintained among hybrid parents. In this context, a continuous search for new CMS‐inducing cytoplasms is necessary. This paper reports detection of maternal inheritance of male sterility in the progeny derived from a natural hybrid between a wild relative [Cajanus lineatus (W. & A.) Maesen comb. nov.] of pigeonpea and an unknown pigeonpea [Cajanus cajan (L.) Millsp.] genotype. In the present study, the male sterility was maintained up to BC₇F₁ generation by an advanced breeding pigeonpea line ICPL 99044. This male sterility inducing cytoplasm of C. lineatus was tagged as A₆. In future, this CMS genetic stock can be used to develop a range of new pigeonpea hybrids with high yield and adaptation.     

Validation of a male‐linked gene locus (OGI) for sex identification in persimmon (Diospyros kaki Thunb.) and its application in F1 progeny

It is crucial to develop a rapid technique for identifying sexuality in the seedling stage of persimmon (Diospyros kaki Thunb.), and the elimination of male progeny has been regarded as an important strategy for enhancing breeding efficiency. In this study, phenotype characterization and genotyping of the male‐linked OGI marker were carried out using 205 accessions, including persimmon cultivars, F₁ progeny and nine related Diospyros species. All persimmon cultivars displayed consistent results regarding OGI amplification and sex phenotype. A total of 143 F₁ progeny were derived from 11 crosses, among which 95 individuals had flowered. In the flowering full‐sib families, the amplification of the OGI marker in agreement with the sex phenotype was obtained in 85 plants (89.5%). The segregation of OGI in ‘Huashi 1’ × ‘Luotian Tianshi’ and ‘Huashi 1’ × Male 3 F₁ populations fit a 1 : 1 ratio. Furthermore, high OGI transferability was observed in nine related species. Overall, the results indicated that the OGI locus could be used to distinguish male from female persimmon plants at an early stage.     

Genetic diversity and population structure of the selected core set in Amaranthus using SSR markers

The genus Amaranthus has gained much attention, particularly for its high economic and nutritional value. It is a genus of taxonomic complexity with many interspecific hybrids. For effective conservation and management of the germplasm collected, the development of a core set of accessions is especially important. A core set of 63 accessions was successfully developed from an entire collection of 634 accessions using the powercore 1.0. Among the tested methods for developing the core set – the advanced M strategy using the modified heuristic method (HCC), randomly chosen collections and stratified random collections – HCC was found to be best, with 100% coverage of alleles and minimum redundancy. Allele frequency distribution of the core set developed with HCC was highly correlated with that of entire collections (r = 0.91). Model‐based structure analysis revealed the presence of three subpopulations and 11 admixtures in the selected core set, which is basically consistent with clustering based on the genetic distance. The results from this study will provide effective information for future germplasm conservation and improvement programmes in Amaranthus.     

Breeding cowpea for resistance to Striga gesnerioides in the Nigerian dry savannas using marker‐assisted selection

Historically, conventional breeding has been the primary strategy used to develop a number of Striga‐resistant varieties currently grown in the Sahel of Western Africa. In this study, we have successfully developed and applied a marker‐assisted selection strategy that employs a single backcross programme to introgress Striga resistance into farmer preferred varieties of cowpea for the Nigeria savannas. In this strategy, we have introduced the Striga resistance gene from the donor parent IT97K‐499‐35 into an elite farmer preferred cowpea cultivar ‘Borno Brown’. The selected 47 BC₁F₂ populations confirmed the recombinants with desirable progeny having Striga resistance gene(s). The 28 lines selected in the BC₁F_2:4 generation with large seed size, brown seed coat colour and carrying marker alleles were evaluated in the field for resistance to Striga resistance. This led to the selection of a number of desirable improved lines that were immune to Striga having local genetic background with higher yield than those of their parents and standard varieties.     

User‐friendly markers linked to Fusarium wilt race 1 resistance Fw gene for marker‐assisted selection in pea

Fusarium wilt is one of the most widespread diseases of pea. Resistance to Fusarium wilt race 1 was reported as a single gene, Fw, located on linkage group III. The previously reported AFLP and RAPD markers linked to Fw have limited usage in marker‐assisted selection due to their map distance and linkage phase. Using 80 F₈ recombinant inbred lines (RILs) derived from the cross of Green Arrow × PI 179449, we amplified 72 polymorphic markers between resistant and susceptible lines with the target region amplified polymorphism (TRAP) technique. Marker–trait association analysis revealed a significant association. Five candidate markers were identified and three were converted into user‐friendly dominant SCAR markers. Forty‐eight pea cultivars with known resistant or susceptible phenotypes to Fusarium wilt race 1 verified the marker–trait association. These three markers, Fw_Trap_480, Fw_Trap_340 and Fw_Trap_220, are tightly linked to and only 1.2 cM away from the Fw locus and are therefore ideal for marker‐assisted selection. These newly identified markers are useful to assist in the isolation of the Fusarium wilt race 1 resistance gene in pea.     

Development of gene‐based markers for the Turnip mosaic virus resistance gene retr02 in Brassica rapa

Turnip mosaic virus (TuMV) is responsible for a serious disease that affects the production of Chinese cabbage. Previous studies have cloned a series of TuMV resistance genes and developed molecular markers. In this study, a derived cleaved amplified polymorphism sequence (dCAPS) marker and a Kompetitive Allele Specific PCR (KASP) marker were developed based on a single recessive gene, retr02, which confers broad‐spectrum TuMV resistance in Chinese cabbage by means of an additional G at the junction of exon 1 and intron 1. The two markers were able to detect the retr02 allele in Chinese cabbage accessions used in breeding programmes. Compared with the dCAPS marker, the KASP marker was flexible, cost‐effective and quick to process, which is likely to be beneficial in establishing high‐throughput assays for marker‐assisted selection.     

Genetic evaluation and selection index in tetraploid Brachiaria ruziziensis

Half‐sib progenies of congo signal grass (Brachiaria ruziziensis Germain & Evrard, syn.: B. eminii, Urochloa ruziziensis) were analysed using a mixed model methodology. The objective was to estimate genetic and phenotypic parameters, predict individual genetic values, estimate correlations between characters associated with biomass production and forage nutritive value and use this information to determine the economic weights to compare three multiplicative selection indices. Individual narrow‐sense heritabilities corrected for inbreeding varied from 0.14 to 0.91 for characters associated with biomass production and from 0.04 a 0.24 for nutritional value characters. The correlations among characters associated with annual biomass production were of high magnitude. In contrast, biomass production characters were negatively correlated with crude protein, acid detergent fibre and lignin. Total dry matter yield, crude protein and regrowth ability were weighted separately in evaluations during wet and dry season or annually in selection indices. Index that considered characters annually resulted in better distribution of forage production along the year than indices that separated wet and dry season production.     

Quantitative trait locus mapping of floral and related traits using an F2 population of Aquilegia

The objective of this study was to determine quantitative trait loci (QTL) underlying ten floral and related traits in Aquilegia. The traits assessed were calyx diameter, corolla diameter, petal length, petal blade length, sepal length, sepal width, spur length, spur width, plant height and flower number. These are important traits for ornamental value and reproductive isolation of Aquilegia. QTL analysis of these traits was conducted using single‐marker analysis and composite interval mapping (CIM). We used an F₂ population consisting of 148 individuals derived from a cross between the Chinese wild species Aquilegia oxysepala and the cultivar Aquilegia flabellata ‘pumila’. Resulting CIM analysis identified 39 QTLs associated with these traits, which were mapped on seven linkage groups. These QTLs could explain 1.22–53.28% of the phenotypic variance. Thirty‐one QTLs, which explained more than 10% of the phenotypic variation, were classified as major QTLs. Graphical representations of the QTLs on seven linkage groups were made. Our research provides the potential for future molecular assisted selection breeding programmes and the cloning of target genes through fine mapping.     

Mapping quantitative trait loci (QTLs) underlying seed vitamin E content in soybean with main,epistatic and QTL × environment effects

Soybean (Glycine max (L.) Merr.) seed contains small amounts of tocopherol, a non‐enzymatic antioxidant known as lipid‐soluble vitamin E (VE). Dietary VE contributes to a decreased risk of chronic diseases in humans and has several beneficial effects on resistance to stress in plants, and increasing VE content is an important breeding goal for increasing the nutritional value of soybean. In this study, quantitative trait loci (QTLs) underlying VE content with main, epistatic and QTL × environment effects were identified in a population of F_5 : 6 recombinant inbred lines from a cross between ‘Hefeng 25’ (a low‐VE cultivar) and ‘OAC Bayfield’ (a high‐VE cultivar). A total of 18 QTLs were detected that showed additive main effects (a) and/or additive × environment interaction effects (ae) in different environments. Moreover, 19 epistatic pairs of QTLs were found to be associated with α‐tocopherol (α‐Toc), γ‐tocopherol (γ‐Toc), δ‐tocopherol (δ‐Toc) and total VE (TE) contents. The QTLs identified in multienvironments could provide more information about QTL by environment interactions and could be useful for the marker‐assistant selection of soybean cultivars with high seed VE contents.     

Genotypic differences in storage losses of sugar beet – causes and indirect criteria for selection

To improve the storability of sugar beets, this study aimed at determining reasons for genotypic variability in sugar losses and invert sugar accumulation during storage, and at identifying indirect criteria to select for varieties with low storage losses prior to storage. In 2011 and 2012, 18 genotypes, and in 2012 and 2013, six genotypes cultivated at two locations were stored for 8 and 12 weeks at 8°C under controlled conditions. The same 18 genotypes were grown under stress conditions in Spain in 2012/2013. Sugar losses were closely correlated with the invert sugar accumulation after storage. Genotypic differences in storage losses were primarily caused by differences in the level of infestation with microorganisms. The invert sugar accumulation was lower for genotypes with high marc concentration before storage, pointing to a non‐specific resistance. Additionally, the sugar concentration in dry matter before storage, and the invert sugar concentration after cultivation under stress conditions correlated with the invert sugar concentration after storage. These parameters are therefore suggested as criteria to select for improved storability of sugar beet genotypes.