Mega‐environment identification for soybean (Glycine max) breeding and production in Brazilian Midwest region

Mega‐environment (ME) identification is the first step for evaluating, selecting and recommending genotypes within a target region (TR). The present study aimed to (a) identify MEs, using GGE biplot methods, in Brazilian edaphoclimatic region (ECR) 402 of soybean cultivation, located in the Mato Grosso State (the TR) and (b) compare the performance of genotypes within the TR and in each ME using fixed and mixed models. Data from three years of soybean yield trials, 19 genotypes and 22 environments were used. The biplots GGE, GGL + GGE and GGS + GGE were implemented to identify the MEs. Two MEs were identified in the TR. ME1 presents a higher altitude, farms which use a higher level of fertilizer inputs and a higher occurrence of the soybean cyst nematode (SCN) than ME2. When selection and recommendation are made based on MEs, genotypes with both broadly and specific adaptation can be selected. This action can improve grain yield in the entire target region.     

Quantitative trait locus analysis for soybean (Glycine max) seed protein and oil concentrations using selected breeding populations

Soybean seed protein and oil concentrations are important traits that directly affect the quality of soyfoods. Many studies and breeding programmes have been conducted to find major quantitative trait loci (QTL) that regulate protein and oil concentrations and to develop soybean cultivars with high protein and/or oil content. The purpose of this study was to identify these QTL using a selected breeding population. The population was tested in field conditions over a period of 3 years. Seed protein and oil concentrations were measured each year. Single‐nucleotide polymorphisms (SNPs) were used to construct genetic map using a 180K SoyaSNP array, which identified 1,570 SNPs. We identified 12 QTL for seed protein, 11 for seed oil concentration and four for both traits. Among these, 17 QTL were closely mapped to previously reported QTL, whereas ten sites were novel. Several QTL were detected across at least two experimental years. These loci are good candidate QTL for optimal seed protein and oil concentrations. Our results demonstrate that favourable target QTL can be successfully identified using selected breeding populations.     

大豆突变体ygl2黄绿叶基因的精细定位

叶片是大豆进行光合碳同化的主要器官,其颜色与光能的捕获力和转化效率有关,也与大豆的产量密切相关。因此,大豆叶色相关基因的挖掘对从光合碳同化途径解析大豆产量问题具有重要意义。黄绿叶是区别于大豆普通绿色叶片的突变类型,是研究大豆叶色相关基因的重要遗传材料。本研究发现了一个黄绿叶突变体ygl2(yellow-green leaf 2),该突变体是由大豆品系GL11自然突变而来,其黄绿叶表型可以稳定遗传。与绿叶野生型GL11相比较,突变体ygl2叶片中叶绿素含量极显著降低,株高、百粒重、蛋白含量均存在显著差异。利用GL11和ygl2构建分离群体,遗传分析表明, ygl2的黄绿叶表型受1对隐性核基因控制,利用分离群体将黄绿叶基因ygl2定位于2号染色体末端SSR标记02₁04到02₁07之间,区间物理距离为56.1 kb,包含9个基因。本研究结果为大豆黄绿叶基因图位克隆及分子标记辅助育种奠定了基础。     

Identification of quantitative trait loci for seed isoflavone concentration in soybean (Glycine max) against soybean cyst nematode stress

Isoflavones are plant secondary metabolites produced in soybean (Glycine max), which provide plant defense against pathogens and are beneficial to human health. Soybean cyst nematode (SCN) is a major yield‐limiting pest in most soybean‐producing area across the world. Traits, seed isoflavones and SCN resistance are quantitative in nature, and their phenotypic evaluations are expensive. Quantitative trait loci (QTL) underlying the two traits will be helpful to develop SCN‐resistant lines with elevated isoflavones using marker‐assisted‐selection (MAS). This study aims to identify isoflavones and SCN‐related QTL in a soybean population consisting of 109 RILs, which was developed from a cross between two commercial soybean cultivars viz. ‘RCAT1004’ and ‘DH4202’ and grown in four non‐SCN and SCN‐infested fields during 2015 and 2016. While single marker ANOVA identified 10 QTL for isoflavones and five for SCN (p < 0.01), simple interval and multiple QTL mappings identified four QTL associated with isoflavones (LOD ≥ 2.2). These results contribute to a better understanding of the genetics of the two traits and provide molecular markers that can be used in MAS to facilitate developing SCN‐resistant soybeans with increased isoflavones.     

Mapping and confirmation of two genes conferring resistance to soybean rust (Phakopsora pachyrhizi) in the soybean line UG-5 (Glycine max)

Development of durable resistance to soybean rust (SBR) is challenging due to the pathogenic diversity of Phakopsora pachyrhizi populations. The objective of this research was to investigate and confirm the genomic locations of Rpp genes in the Ugandan line UG-5 that confer resistance to different SBR pathotypes. Bulked segregant analysis revealed two genomic regions associated with resistance in a cross with rust-susceptible 'Williams 82'. Composite interval mapping in the F₂ and F_2:3 populations had a LOD score of 48.7 in a region 0.38 cM away from the estimated location of the Rpp1 locus on chromosome (Chr.) 18. An approximately 23-Kbp interval spanning the Rpp1 locus was flanked by SNP markers ss715632313 and ss715632318. Another interval was identified at the Rpp3 locus on Chr. 6 between markers Satt100 and ss715594488 (2.4 cM) in the F₂ population and between Satt100 and ss715594874 (4.3 cM) in the F_2:3 population, with a maximum LOD score of 25.6. UG-5 was thus confirmed to have SBR resistance genes at the Rpp1 and Rpp3 loci that can be pyramided into other elite cultivars.     

Mapping quantitative trait loci for yield-related traits in soybean (Glycine max L.)

Development of soybean cultivars with high seed yield is a major focus in soybean breeding programs. This study was conducted to identify genetic loci associated with seed yield-related traits in soybean and also to clarify consistency of the detected QTLs with QTLs found by previous researchers. A population of 135 F_2:3 lines was developed from a cross between a vegetable soybean line (MJ0004-6) and a landrace cultivar from Myanmar ({"type":"entrez-nucleotide","attrs":{"text":"R18500","term_id":"772110","term_text":"R18500"}}R18500). They were evaluated in the experimental field of Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand in a randomized complete block design with two replications each in 2011 and 2012 growing seasons. The two parents exhibited contrasting characteristics for most of the traits that were mapped. Analysis of variance showed that the main effects of genotype and environment (year) were significant for all studied traits. Genotype by environment interaction was also highly significant for all the traits. The population was genotyped by 149 polymorphic SSR markers and the genetic map consisted of 129 SSR loci which converged into 38 linkage groups covering 1156 cM of soybean genome. There were 10 QTLs significantly associated with seed yield-related traits across two seasons with single QTLs explaining between 5.0% to 21.9% of the phenotypic variation. Three of these QTLs were detected in both years for days to flowering, days to maturity and 100 seed weight. Most of the detected QTLs in our research were consistent with earlier QTLs reported by previous researchers. However, four novel QTLs including SF1, SF2 and SF3 on linkage groups L and N for seed filling period and PN1 on linkage group D1b for pod number were identified in the present study.     

DNA fingerprinting in soybean (Glycine max (L.) Merrill) with oligonucleotide probes for simple repetitive sequences

Summary Soybean DNA fingerprints were analyzed by digoxigenin-labeled oligonucleotide probes complementary to simple repetitive sequences. The clearest and most polymorphic patterns were obtained with (AAT)₆ as a probe, with which all 47 soybean cultivars tested could be distinguished. However, DNA fingerprints of individuals within cultivars showed the same pattern. Using (CT)₈, (GAA)₅ or (AAGG)₄ as probes, clear polymorphic patterns among cultivars and accessions in the subgenus Soja (Glycine max and Glycine soja) were not observed, while quite different patterns were found in accessions in the subgenus Glycine. The results suggest that G. max and G. soja are closer in their genome structure. DNA fingerprints of reciprocal crosses between cultivars and accessions in the subgenus Soja were similar, and contained bands of both parents. In an F₂ population from these crosses, such bands segregated in a Mendelian fashion.     

Identification of quantitative trait loci and candidate genes controlling the tocopherol synthesis pathway in soybean (Glycine max)

A recombinant inbred line (RIL) population was used to identify quantitative trait loci (QTLs) and their candidate genes controlling the tocopherol (Toc) synthesis pathway. The RIL population was cultivated in field conditions in 3 years. A genetic map constructed using 1624 DNA markers was used for QTL analysis. We identified 22 QTLs for seed tocopherol contents and their ratios, of which two QTL clusters on chromosomes (Chr) 9 and 14 exerted consistent large effects on tocopherol composition across the 3 years. The QTL cluster localized on Chr 9 might correspond to γ-TMT3, which controls the conversion of γ-Toc into α-Toc. The QTL cluster localized on Chr 14 was novel, which might regulate the conversion of MPBQ (a precursor of δ-Toc) into DMPBQ (the precursor of γ-Toc). The effect of the QTL cluster on Chr 14 was validated in a pair of near isogenic lines, and its candidate gene was mined. The identified QTLs and their candidate genes might be used in breeding programmes to improve α-Toc content in soybean seeds.     

Genetic variation in soybean (Glycine max (L.) Merril) for cookability and water absorption during cooking

Summary Improvement of cookability is an important objective in breeding of food legumes. The present study was undertaken to investigate variation in cookability in soybean. Genetic variation was observed among lines from two crosses. Absence of associations between cookability and protein content, oil content and grain yield indicate that selection for cookability can be achieved without adversely affecting the expression of these characters.     

Parent genome contribution and its relationship with grain yield in backcross-derived lines of soybean (Glycine max)

Introgression of yellow mosaic disease (YMD) resistance and effect of recurrent parent genome (RPG) on grain yield was studied in 84 soybean genotypes from four populations namely, F_2:7, BC₁F₆, BC₂F₅ and BC₃F₄ derived from cross JS335 x SL525. It was observed that in F_2:7, BC₁F₆, BC₂F₅ and BC₃F₄ derived lines, RPG contribution was 42.5%, 54.9%, 66.4% and 77.6%, respectively, which is significantly less than expected values. Linkage drag from donor parent with YMD resistance gene may be a possible reason for such deviations. Average grain yield per plant in F_2:7, BC₁F₆, BC₂F₅ and BC₃F₄ generations was observed as 13.0, 14.3, 14.9 and 16.1 g, respectively. It was observed that genotypes with more than 80% RPG observed to have both YMD resistance and good yield potential. Graphical genotyping (GGT) analysis revealed that maximum RPG was recovered in chromosomes 8 and 10 and maximum introgression occurred in chromosomes 6 and 19. Our results demonstrated that RPG was positively associated with yield as evident from yield increase with increase in RPG.     

QTL mapping of phosphorus deficiency tolerance in soybean (Glycine max L. Merr.)

Phosphorus (P) deficiency is a major abiotic stress that limits plant growth and crop productivity throughout the world. In the present study, 184 recombinant inbred line (RIL) families developed from soybean varieties Kefeng No. 1 and Nanong 1138-2 were used to identify quantitative trait loci (QTL) associated with P deficiency tolerance. Seven traits of plant height (HT), weight of fresh shoot (FSW), weight of fresh root (FRW), weight of dry root (DRW), length of main root (RL), phosphorus content in leaf (LP), phosphorus content in root (RP), were used as parameters to assess the phosphorus deficiency tolerance. The QTL mapping for the seven traits was performed using the program WinQTLCart. Seven QTLs were detected and mapped on two linkage groups for three traits of weight of fresh shoot, phosphorus contents in leaf and in root. The QTLs that had LOD scores more than three were detected for all of the three traits above. Most of the QTLs explained more than 10% of the total variation. The two QTLs for phosphorus content in leaf explained more than 20% of the total variation, respectively. Five QTLs were mapped on linkage group F2, and two on linkage F1. It was suggested that the genes related to phosphorus deficiency tolerance located on linkage group F in soybean.Contributed equally to this work.     

Effect of intercropping on rhizosphere population in maize (Zea mays L.) and soybean (Glycine max Merill)

Comparative studies on the rhizosphere and non-rhizosphere bacterial and fungal populations of maize and soybean both under solecropping and intercropping were conducted. Intercropping increased the bacterial R : S ratio of maize and soybean, whereas fungal R : S ratio showed a decrease in both cases when compared to solecrop condition. Intercropping of maize with soybean increased the maize yield by 34% and decreased the soybean yield by 51% when compared with their respective yields under solecrop conditions. The dominant fungal species in the rhizosphere and non-rhizosphere soils were also affected by plant species and cropping systems.     

Variation in the photoperiodic response on several characters in soybean,Glycine max (L.) Merrill

Summary The photoperiodic response on 12 characters in 40 soybean, Glycine max (L.) Merrill, cultivars were investigated using 10-hour (short day) and 16-hour (long day) photoperiods. Seventeen cultivars showed no significant difference between photoperiods for all 12 characters. Seven cultivars showed significant difference for only one trait. Phenotypic changes in 17 cultivars may be due to factors other than photoperiod. Number of pods per plant, days to maturity, and number of nodes per plant were highly correlated with yield per plant in both photoperiods. Invariably, the cultivars which had significant differences in the numbers of flowers produced per plant between the two photoperiods also had significant differences in the numbers of pods per plant and yield. First node to flower, plant height at flowering, days to flowering, nodes at flowering, and the 100-seed weight were least influenced by the photoperiods in most of the cultivars, while the height at maturity, number of nodes at maturity, number of days to maturity, and yield were most influenced.AVRDC Journal paper 46 (78–88).     

Yield stability studies of soybean (Glycine max (L.) Merrill) under rhizobia inoculation in the savanna region of Nigeria

Soybean (Glycine max (L.) Merrill) production is expanding into temperate and tropical environments. Yield stability studies under rhizobia inoculation were investigated in 24 soybean genotypes over two successive growing seasons at three agro‐ecological zone of Nigeria, during the 2015–2016 rainy seasons. Treatments were arranged in a split‐plot design and replicated three times. Treatments were 24 soybean genotypes and three levels of rhizobia inoculation. Results indicated that the variation of genotypes and inoculation on percentage emergence, height, number of leaves, number of branches per plant, total biomass yield, above‐ground biomass and seed yield was significant (p = .05). The effects of genotypes (G), environment (E) and G × E interactions on seed yield were also significant. Two soybean genotypes (TGx 1989‐45F and TGx 1990‐110FN) were identified as the most promising in relation to yield stability. Of the three locations, Abuja produced the least interaction effects followed by Igabi and may be most appropriate environments for large‐scale soybean production. Appropriate inoculation of soybean with inoculants (LegumeFix and or NoduMax) should be encouraged in farmer's field.     

Tagging the juvenile locus in soybean [Glycine max (L.) Merr.] with molecular markers

Soybean cultivars carrying the `long juvenile trait' show a delayed flowering response under short day conditions. The incorporation of this character into genotypes of agronomic interest may allow a broader range of sowing dates and latitudes for a single cultivar adaptation. The objective of this work was to identify molecular markers linked to the juvenile locus in soybean. Experiments were carried out using two pairs of near isogenic lines(NILs) differing in the presence of the long juvenile trait, and RAPD markers. Four hundred primers were first screened to find polymorphism associated with the trait. Additional differences between NILs were sought by digesting the genomic DNA with five restriction enzymes. Polymorphic fragments detected between NILs were tested for linkage to the juvenile locus in the corresponding F₂ segregating populations. Marker bc357-HaeIII was linked (χ²L = 46.316) to the juvenile locus with an estimated recombination frequency of 0.13 ± 0.03in one of the genetic backgrounds studied. The fragment was cloned, sequenced and converted into a SCAR marker. Moreover,bc357-HaeIII was used as RFLP probe. Both, SCAR and RFLP generated markers linked to the juvenile locus in the two genetic backgrounds analysed. Results presented in this work can be utilised for both, the localisation of the gene associated with the character and for tagging the juvenile trait in soybean breeding programs. This revised version was published online in August 2006 with corrections to the Cover Date.     

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.     

Molecular mapping of two recessive genes controlling resistance to bacterial leaf pustule disease in soybean (Glycine max)

Bacterial leaf pustule (BLP) caused by Xanthomonas axonopodis pv. glycines (Xag) is a serious soybean disease. A BLP resistant genotype ‘TS-3’ was crossed with a BLP susceptible genotype ‘PK472’, and a segregating F₂ mapping population was developed for genetic analysis and mapping. The F₂ population segregation pattern in 15:1 susceptible/resistance ratio against Xag inoculum indicated that the resistance to BLP in ‘TS-3’ was governed by two recessive genes. A total of 12 SSR markers, five SSR markers located on chromosome 2 and seven SSR markers located on chromosome 6 were identified as linked to BLP resistance. One of the resistance loci (r1) was mapped with flanking SSR markers Sat_183 and BARCSOYSSR_02_1613 at a distance of 0.9 and 2.1 cM, respectively. Similarly, SSR markers BARCSOYSSR_06_0024 and BARCSOYSSR_06_0013 flanked the second locus (r2) at distances of 1.5 and 2.1 cM, respectively. The identified two recessive genes imparting resistance to BLP disease and the SSR markers tightly linked to these loci would serve as important genetic and molecular resources to develop BLP resistant genotypes in soybean.     

Insect-mediated cross-pollination in soybean [Glycine max (L.) Merrill]: II. Phenotypic recurrent selection

Recurrent selection is a method for population improvement which has been used in soybean [Glycine max (L.) Merrill] to modify traits such as grain yield, seed-protein content, seed-oil content, tolerance to iron-deficiency chlorosis, and seed size. Nuclear male-sterility with insect-mediated cross-pollination has been successfully used in recurrent selection schemes in soybean. However, little attention has been given to selection to increase the agronomic performance of male-sterile plants per se. The objective of this study was to evaluate the response of male-sterile lines segregating for male-sterile alleles ms2, ms3, ms6, ms8, and ms9 to phenotypic recurrent selection for increased seed-set after 3 cycles, using a selected group of male parents. Bees halictidae, anthophoridae, andrenidae, and megachilidae were utilized as the pollinator vector. The results indicated that recurrent selection in a favorable environment was successful to increase the number of seeds per male-sterile plant. Although a differential response was observed among populations, the seed-set observed would justify the use of some specific male-sterile selections as female parents in a hybrid soybean seed production system.     

Combining ability of soybean (Glycine max) for low phosphorus tolerance on acidic soils of Western Ethiopia

Determining the gene actions governing the inheritance of traits of interest has paramount importance in designing a breeding approach to improve the progeny populations. This study was undertaken to determine the combining ability of nine selected parental lines in the F₂/F₃ segregating populations for low P tolerance. The experiment was laid out in an alpha lattice design in two locations, that is Mettu and Assossa of Western Ethiopia that are characterized by soils with low P and pH. General combining ability (GCA) effects were highly significant for grain yield, pod length, days to maturity and plant height, while specific combining ability (SCA) effects were highly significant for grain yield, 100-seed weight, pod length and plant height. The parent Hardee-1 was identified as the best general combiner for yield, number of seeds per pod, pod length, plant height and pod number. The results suggest that additive gene action was important for several of the studied traits, implied by significant GCA effect, which might indicate selection for these traits could be effective in later segregating generations.