Mapping and use of QTLs controlling pod dehiscence in soybean

While the cultivated soybean, Glycine max (L.) Merr., is more recalcitrant to pod dehiscence (shattering-resistant) than wild soybean, Glycine soja Sieb. & Zucc., there is also significant genetic variation in shattering resistance among cultivated soybean cultivars. To reveal the genetic basis and develop DNA markers for pod dehiscence, several research groups have conducted quantitative trait locus (QTL) analysis using segregated populations derived from crosses between G. max accessions or between a G. max and G. soja accession. In the populations of G. max, a major QTL was repeatedly identified near SSR marker Sat_366 on linkage group J (chromosome 16). Minor QTLs were also detected in several studies, although less commonality was found for the magnitudes of effect and location. In G. max × G. soja populations, only QTLs with a relatively small effect were detected. The major QTL found in G. max was further fine-mapped, leading to the development of specific markers for the shattering resistance allele at this locus. The markers were used in a breeding program, resulting in the production of near-isogenic lines with shattering resistance and genetic backgrounds of Japanese elite cultivars. The markers and lines developed will hopefully contribute to the rapid production of a variety of shattering-resistant soybean cultivars.     

Identification and confirmation of quantitative trait loci for stachyose content in soybean seed

Stachyose is an unfavorable sugar in soybean meal that causes flatulence for non‐ruminant animals. Understanding the genetic control of stachyose in soybean will facilitate the modification of stachyose content at the molecular level. The objective of this study was to identify quantitative trait loci (QTL) associated with seed stachyose content using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. A normal stachyose cultivar, ‘Osage’, was crossed with a low stachyose line, V99‐5089, to develop a QTL mapping population. Two parents were screened with 33 SSR and 37 SNP markers randomly distributed on chromosome 10, and 20 SSR and 19 SNP markers surrounding a previously reported stachyose QTL region on chromosome 11. Of these, 5 SSR and 16 SNP markers were used to screen the F_3:4 lines derived from ‘Osage’ x V99‐5089. Seed samples from F_3:5 and F_3:6 lines were analyzed for stachyose content using high‐performance liquid chromatography (HPLC). Composite interval mapping analysis indicated that two stachyose QTL were mapped to chromosome 10 and 11, explaining 11% and 79% of phenotypic variation for stachyose content, respectively. The SSR/SNP markers linked to stachyose QTL could be used in breeding soybean lines with desired stachyose contents. Chi‐square tests further indicated that these two QTL probably represent two independent genes for stachyose content. Therefore, a major QTL was confirmed on chromosome 11 and a novel QTL was found on chromosome 10 for stachyose content.     

Molecular mapping of soybean seed tocopherols in the cross ‘OAC Bayfield’ × ‘OAC Shire’

Soybean (Glycine max [L.] Merr.) is cultivated primarily for its protein and oil in the seed. In addition, soybean seeds contain nutraceutical compounds such as tocopherols (vitamin E), which are powerful antioxidants with health benefits. The objective of this study was to identify molecular markers linked to quantitative trait loci (QTL) that affect accumulation of soybean seed tocopherols. A recombinant inbred line (RIL) population derived from the cross ‘OAC Bayfield’ × ‘OAC Shire’ was grown in three locations over 2 years. A total of 151 SSR markers were polymorphic of which a one‐way analysis of variance identified 42 markers whereas composite interval mapping identified 26 markers linked to tocopherol QTL across 17 chromosomes. Individual QTL explained from 7% to 42% of the total phenotypic variation. Significant two‐locus epistatic interactions were identified for a total of 122 combinations in 2009 and 152 in 2010. The multiple‐locus models explained 18.4–72.2% of the total phenotypic variation. The reported QTL may be used in marker‐assisted selection (MAS) to develop high tocopherol soybean cultivars.     

Population-specific QTLs and their different epistatic interactions for pod dehiscence in soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.]

Pod dehiscence (PD) prior to harvest results in serious yield loss in soybean. Two linkage maps with simple sequence repeat (SSR) markers were independently constructed using recombinant inbred lines (RILs) developed from Keunolkong (pod-dehiscent) × Sinpaldalkong (pod-indehiscent) and Keunolkong × Iksan 10 (pod-indehiscent). These soybean RIL populations were used to identify quantitative trait loci (QTLs) conditioning resistance to PD. While a single major QTL on linkage group (LG) J explained 46% of phenotypic variation in PD in the Keunolkong × Sinpaldalkong population with four minor QTLs, three minor QTLs were identified in the Keunolkong × Iksan 10 population. Although these two populations share the pod dehiscent parent, no common QTL has been identified. In addition, epistatic interactions among three marker loci partially explained phenotypic variation in PD in both populations. The result of this study indicates that different breeding strategies will be required for PD depending on genetic background.     

Genetic mapping of quantitative trait loci conditioning salt tolerance in wild soybean (Glycine soja) PI 483463

Salt tolerance in soybean [Glycine max (L.) Merr.] is controlled by major quantitative trait loci (QTL) or single gene(s). Among soybean germplasm, wild soybean plant introduction PI 483463 was reported to have a single dominant gene for salt tolerance. The objective of this study was to genetically map the QTL in a recombinant inbred line (RIL) population derived from a cross between PI 483463 and Hutcheson. Simple sequence repeat (SSR) markers and universal soybean single nucleotide polymorphism (SNP) panel (the USLP 1.0) were utilized for molecular genotyping. The RILs were phenotyped in two independent tests in a greenhouse using a 1–5 scale visual rating method. The results showed that the salt tolerant QTL in PI 483463 was mapped to chromosome 3 in a genomic region between the Satt255 and BARC-038333-10036 markers. The favorable allele inherited from PI 483463 conferred tolerance to salinity and had an additive effect on reducing leaf scorch. A subset of 66 iso-lines was developed from the F₃ families of the same cross and was used for genetic confirmation of the QTL. The integration of recombination events and the salt reaction data indicate that the QTL is located in the region of approximately a 658 kb segment between SSR03_1335 at nucleotide 40,505,992 and SSR03_1359 at nucleotide 41,164,735 on chromosome 3. This narrow region can facilitate further genomic research for salt tolerance in soybean including cloning salt tolerance genes.     

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.     

Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat

The objectives of this study were to validate the major quantitative trait locus (QTL) for scab resistance on the short arm of chromosome 3B in bread wheat and to isolate near‐isogenic lines for this QTL using marker‐assisted selection (MAS). Two resistant by susceptible populations, both using ‘Ning7840’ as the source of resistance, were developed to examine the effect of the 3BS QTL in different genetic backgrounds. Data for scab resistance and simple sequence repeat (SSR) markers linked to the resistance QTL were analyzed in the F_2:3 lines of one population and in the F_3:4 lines of the other. Markers linked to the major QTL on chromosome 3BS in the original mapping population (‘Ning7840’/‘Clark’) were closely associated with scab resistance in both validation populations. Marker‐assisted selection for the QTL with the SSR markers combined with phenotypic selection was more effective than selection based solely on phenotypic evaluation in early generations. Marker‐assisted selection of the major QTL during the seedling stage plus phenotypic selection after flowering effectively identified scab resistant lines in this experiment. Near‐isogenic lines for this 3BS QTL were isolated from the F₆ generation of the cross ‘Ning7840’/‘IL89‐7978’ based on two flanking SSR markers, Xgwm389 and Xbarc147. Based on these results, MAS for the major scab resistance QTL can improve selection efficiency and may facilitate stacking of scab resistance genes from different sources.     

Identification of quantitative trait loci underlying soybean (Glycine max [L.] Merr.) seed weight including main,epistatic and QTL × environment effects in different regions of Northeast China

Seed weight (SW) is the important soybean (Glycine max [L.] Merr.), yield component and also affected the quality of soybean‐derived foods. The aim of this study was to identify the quantitative trait loci (QTL) underlying SW through 112 recombinant inbred lines (RILs) derived from the cross between “Zhongdou27” (G. max, designated by its bigger seed size, 21.9 g/100 seeds) and “Jiunong 20” (G. max, smaller seed size, 17.5 g/100 seeds). Phenotypic data were collected from this RIL population after it was grown in the sixteen tested environments. A total of eight QTL (QSW1‐1, QSW2‐1, QSW2‐2, QSW5‐1, QSW15‐1, QSW17‐1, QSW19‐1 and QSW20‐1) were identified, and they could explain 4.23%–14.65% of the phenotypic variation. Among these eight QTL, three QTL (QSW1‐1 located on the interval of Sat_159‐Satt603 of chromosome (Chr) 1 (LGD1a), QSW19‐1 located on the interval of Sat_340‐Satt523 of Chr 19 (LGL) and QSW20‐1 located on Sat_418‐Sat_105 of Chr 20 (LGI)) were newly identified and could explain 4.235%–10.08%, 8.45%–13.49% and 8.08%–10.18% of the phenotypic variation, respectively. Six of the eight identified QTL including QSW2‐2, QSW5‐1, QSW15‐1, QSW17‐1, QSW19‐1 and QSW20‐1 exhibited a significant additive (a) effect, while two QTL (QSW2‐1 and QSW19‐1) only displayed significant additive‐by‐environment (ae) effects. A total of four epistatic pairwise QTL for SW were identified in the different environments. These eight QTL and their genetic information obtained here were valuable for molecular marker‐assisted selection and the realization of a reasonable SW breeding programme in soybean.     

抗青枯病兼大果和高出仁率的花生新种质创制

青枯病是影响花生产量和品质的重要土传性细菌病害,百果重和出仁率是与花生产量相关的重要性状。本研究利用远杂9102和徐州68-4杂交构建的RIL群体,在B02染色体上定位到青枯病抗性主效QTL qBWRB02。结合前期对百果重和出仁率QTL的定位结果发现,所涉及的3个性状的主效QTL分布在不同的染色体上。以RIL群体基因型数据和多个环境的青枯病抗性、百果重和出仁率表型数据为基础,利用与主效QTL紧密连锁分子标记筛选出6份聚合抗青枯病、荚果大、出仁率高3种优良性状的新种质,可以作为育种中间材料或亲本培育高产抗病新品种。本研究利用分子标记辅助选择和表型鉴定相结合有效筛选抗病高产种质,为未来花生育种提供了新思路。     

Identification of novel QTL for leaf traits in soybean

Several leaf traits of soybean (Glycine max L. Merr.), including leaf area (LA), leaf shape (LS) and specific leaf weight (SLW) may be related to soybean yield. The objective of this study was to identify novel quantitative trait loci (QTL) for LA, LS and SLW in a recombinant inbred line (RIL) population. The phenotype data were collected in 2011 and 2012 for 93 F_7:10 RILs using a randomized complete block design with 2 replicates each year. Five hundred and sixteen single‐nucleotide polymorphism (SNP) markers and the phenotype data were used to detect QTL using single marker analysis (SMA) and composite interval mapping (CIM). Single markers analysis identified 26 QTL for the three traits, of which 17 were novel and the rests were previously reported QTL. Most of these QTL were also identified by CIM. Most QTL reported in this study were in close proximity (<1 cM) of one or more SNP markers. These publicly available SNP markers with close linkage to LA, LS and SLW should be useful for marker‐assisted breeding for these traits.     

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.     

Genetic studies on saline and sodic tolerances in soybean

Salt-affected soils are generally classified into two main categories: saline and sodic (alkaline). Developing and using soybean (Glycine max (L.) Merr) cultivars with high salt tolerance is an effective way of maintaining sustainable production in areas where soybean growth is threatened by salt stress. Early classical genetics studies revealed that saline tolerance was conditioned by a single dominant gene. Recently, a series of studies consistently revealed a major quantitative trait locus (QTL) for saline tolerance located on linkage group N (chromosome 3) around the SSR markers Satt255 and Sat_091; other minor QTLs were also reported. In the case of sodic tolerance, most studies focused on iron deficiency caused by a high soil pH, and several QTLs associated with iron deficiency were identified. A wild soybean (Glycine soja Sieb. & Zucc.) accession with high sodic tolerance was recently identified, and a significant QTL for sodic tolerance was detected on linkage group D2 (chromosome 17). These studies demonstrated that saline and sodic tolerances were controlled by different genes in soybean. DNA markers closely associated with these QTLs can be used for marker-assisted selection to pyramid tolerance genes in soybean for both saline and sodic stresses.     

Quantitative trait loci associated with lodging tolerance in soybean cultivar ‘Toyoharuka’

Lodging tolerance (LT) is an important trait for high yield and combine-harvesting efficiency in soybean [Glycine max (L.) Merr.]. Many previous studies have investigated quantitative trait loci (QTLs) for lodging score (LS) in soybean. Most of the investigated QTLs were located in the proximal region of maturity or growth habit loci. The aim of this study was to identify genetic factors for LT not associated with maturity or growth habit. QTL analysis was performed using a recombinant inbred line (RIL) population derived from a cross between ‘Toyoharuka’ (TH), a lodging-tolerant cultivar, and ‘Toyomusume’ (TM). The genotypes of TH and TM were estimated as both e1e2E3E4 and dt1. The average LS over 4 years was used for QTL analysis, identifying a major and stable QTL, qLS19-1, on chromosome 19. The LS of the near-isogenic line (NIL) with the TH allele at Sat_099, the nearest marker to qLS19-1, was significantly lower than the NIL with the TM allele at that position. The TH allele at Sat_099 rarely had a negative influence on seed yield or other agronomic traits in both NILs and the TM-backcrossed lines. Our results suggest that marker-assisted selection for qLS19-1 is effective for improving LT in breeding programs.     

大豆品种豫豆25抗疫霉根腐病基因的鉴定

大豆疫霉根腐病是大豆破坏性病害之一。防治该病的最有效方法是利用抗病品种。迄今,已在大豆基因组的9个座位鉴定了15个抗大豆疫霉根腐病基因,但是只有少数基因如Rps1c、Rps1k抗性在我国是有效的。因此,必需发掘新的抗疫霉根腐病基因,以满足抗病育种的需求。豫豆25具有对大豆疫霉菌的广谱抗性,是目前筛选出的最优异的抗源。以豫豆25为抗病亲本分别与豫豆21和早熟18杂交构建F_2:3家系群体。两个群体的抗性遗传分析表明,豫豆25对疫霉根腐病的抗性由一个显性单基因控制,暂定名为RpsYD25。用SSR标记分析两个群体,RpsYD25均被定位于大豆分子遗传图谱N连锁群上。由于Rps1座位已作图在N连锁群,选择Rps1k基因中的一些SSR设计引物,检测RpsYD25与Rps1座位的遗传关系。结果表明,一个SSR标记Rps1k6与RpsYD25连锁,二者之间的遗传距离为19.4 cM。因此,推测RpsYD25可能是Rps1座位的一个新等位基因,也可能是一个新的抗病基因。     

Molecular mapping of a major QTL conferring resistance to SCMV based on immortal RIL population in maize

Sugarcane mosaic virus (SCMV) is one of devastating pathogens in maize (Zea mays L.), and causes serious yield loss in susceptible cultivars. An effective solution to control the virus is utilizing resistant genes to improve the resistance of susceptible materials, whereas the basic work is to analyze the genetic basis of resistance. In this study, maize inbred lines Huangzao4 (resistant) and Mo17 (susceptible) were used to establish an F₉ immortal recombinant inbred line (RIL) population containing 239 RILs. Based on this segregation population, a genetic map was constructed with 100 simple sequence repeat (SSR) markers selected from 370 markers, and it covers 1421.5 cM of genetic distance on ten chromosomes, with an average interval length of 14.2 cM. Analysis of the genetic map and resistance by mapping software indicated that a major quantitative trait locus (QTL) was between bin6.00 and bin6.01 on chromosome 6, linked with marker Bnlg1600 (0.1 cM of interval). This QTL could account for 50.0% of phenotypic variation, and could decrease 27.9% of disease index.     

陆地棉重组近交系“中G6” QTL的初步定位

 利用2个陆地棉种质材料爱字棉1517与德州047构建了重组近交系。田间调查显示,两亲本田间性状差异多数达到显著或极显著,群体性状数据完全符合受多位点控制的数量性状遗传的特征。分子标记多态性筛选结果表明,两亲本亲缘关系相对较近,利用SSR构建高密度遗传连锁图有一定困难,但对于所定位的QTL位点,其准确性将会有一定程度提高。试验构建了一张包括51个标记分为15个连锁群的遗传连锁图,总长504.05 cM,覆盖棉花基因组总长度的10.08%。利用两年田间数据检测到QTL位点15个,其中生育期性状3个,纤维品质性状7个,产量性状5个。与标记图距在1 cM以内的QTL位点7个,这将对分子标记辅助育种具有一定的参考价值。     

大豆种粒斑驳抗性的遗传分析及基因定位

运用SSR标记技术及分离群体组群分析法(BSA法), 对大豆品系3C624×东农8143的F₂、F₃代群体接种SMV1号株系鉴定种粒斑驳抗性, 并进行抗种粒斑驳基因的分子定位。结果表明, 东农8143对SMV1号株系的种粒斑驳抗性受1对显性基因控制。用Mapmaker/Exp 3.0b进行连锁分析, 抗种粒斑驳基因位于大豆染色体组的F连锁群上, 并获得了与抗种粒斑驳基因紧密连锁的5个SSR标记Sat_297、Sat_229、Sat_317、Satt335和Sct_188, 标记与抗病基因间的排列顺序和连锁距离为Sat_297–12.4 cM–Sat_229–3.6 cM–SRSMV1–1.7 cM–Sat_317–2.4 cM– Satt335–13.8 cM–Sct_188。其中近距离标记Sat_229(3.6 cM)、Sat_317(1.7 cM)和Satt335(4.1 cM)可用于标记辅助选择育种和抗源筛选。     

Molecular tagging of Asiatic soybean rust resistance in exotic genotype EC 241780 reveals complementation of two genes

Asian soybean rust (ASR) caused by Phakopsora pachyrhizi severely reduces seed yield in soybean. Molecular tagging of ASR resistance can help in the process of resistance breeding. In this study, an F₂ population of cross (susceptible cultivar ‘NRC 7’ × resistant exotic genotype EC 241780) was used for bulked segregant analysis (BSA) with 25 SSR (simple sequence repeat) primers linked with six Rpp genes. Among them, five polymorphic SSR markers, viz., Sct 187, SSR 1859, Satt 191 (Rpp1b like loci) and Satt 215, Sat_361 (Rpp2 loci) distinguished the ASR resistant and susceptible bulks and individuals. In combined marker analysis, the markers Satt 191 (Rpp1b like loci) and Satt 215 (Rpp2 loci) were linked with ASR severity score and were also confirmed in individual 110 F₂ segregants. Hence, these markers could be utilized in the marker assisted rust resistance breeding of Rpp1b like and Rpp2 genes. In silico candidate gene analysis for hypersensitive response revealed that Satt 191 linked region was rich in genes encoding apoptotic ATPase having leucine‐rich repeat (LRR) domain.     

Modifier QTL for fatty acid composition in soybean oil

Soybean [Glycine max (L.) Merr.] is the principal oilseed crop in the world. Soybean oil has various industrial and food applications. The quality of soybean oil is determined by its fatty acid composition. Palmitic, stearic, oleic, linoleic and linolenic are the predominant fatty acids in soybean oil. The objective of this study was to determine the associations of simple sequence repeat (SSR) molecular markers with minor differences in fatty acids in soybean oil thereby detecting modifier quantitative trait loci (QTL) which could further improve soybean oil quality. To achieve this objective, 101 F₆-derived recombinant inbred lines (RIL) from a population whose parents did not contain major mutant fatty acid alleles were developed from a cross of N87-984-16 × TN93-99. Fatty acids were determined by gas chromatography. Heritability estimates on an entry mean basis for fatty acids ranged from 65.8 to 77.3% for palmitic and linoleic acids, respectively. Molecular marker Satt537 located on molecular linkage group (MLG) D1b was associated with palmitic acid and Satt168 and Satt249 located on MLG B2 and J, respectively were associated with stearic acid. Molecular markers Satt185 or Satt268 (which are within 0.6 cM of each other) located on MLG E were consistently associated with oleic and linoleic acid, and Satt263 and Satt235 located on MLG E and G, respectively were associated with linolenic acid. The lack of markers associated with multiple fatty acids suggests the possibility of independently changing fatty acid levels to achieve a desirable composition, except for regions common to all saturated fatty acids. Phenotypic variation explained by the fatty acids modifier QTL ranged from 10 to 22.5%. These modifier QTL may be useful in making minor improvements to further enhance the quality of soybean oil.     

Fine mapping of the major Soybean dwarf virus resistance gene Rsdv1 of the soybean cultivar ‘Wilis’

Soybean dwarf virus (SbDV), a Luteoviridae family member, causes dwarfing, yellowing and sterility of soybean (Glycine max), leading to one of the most serious problems in soybean production in northern Japan. Previous studies revealed that the Indonesian soybean cultivar ‘Wilis’ is resistant to SbDV and that the resistance can be introduced into Japanese cultivars. A major QTL for SbDV resistance has been reported between SSR markers Sat_217 and Satt211 on chromosome 5. In this study, we named this QTL Rsdv1 (resistance to SbDV) and developed near-isogenic lines incorporating Rsdv1 (Rsdv1-NILs) using Sat_217 and Satt211 markers. The Rsdv1-NILs were resistant to SbDV in greenhouse inoculation and field tests, indicating that Rsdv1 alone is sufficient for the resistance phenotype. We fine-mapped Rsdv1 within the 44-kb region between Sat_11 and Sct_13. None of the six genes predicted in this region was closely related to known virus resistance genes in plants. Thus, Rsdv1 may confer resistance by a previously unknown mechanism. We suggest that Rsdv1 may be a useful source for the Japanese soybean breeding program to introduce SbDV resistance.