Construction of Genetic Linkage Map of Bread Wheat （Triticum aestivum L.） Using an Intervarietal Cross and QTL Map for Spike Related Traits

Most often a genetic linkage map is prepared using populations obtained from two highly diverse genotypes. However, the markers from such a map may not be useful in a breeding program as these markers may not be polymorphic among the varieties used in breeding. For the past nine years, intraspecific maps have been gaining importance and such maps based on Swiss （PaiUard et al., 2003）, Japanese （Suenaga et al., 2005）, Australian （Chaimcrs et al., 2001） wheat varieties arc available. A map based on Indian wheat varieties however has not been reported. We constructed a genetic linkage map based on a cross between two Indian bread wheat （Triticum aestivum L.） varieties, Sonalika and Kalyansona. One hundred and fifty F2 individuals were analyzed for arbitrarilyprimed polymerase Chain reaction （AP-PCR）, random amplified polymorphic DNA （RAPD）, inter simple sequence repeats （ISSR）, Sequence Tagged Microsatelhte Sites （STMS）, Amplified Fragment Length Polymorphism （AFLP） markers, seed storage proteins and known genes. A linkage map was constructed consisting of 236 markers and spanning a distance of 3 639 cM with 1 211.2 cM for A genome, 1 669.2 cM for B genome, 192.4 cM for D genome and 566.2 cM for unassigned groups,     

Molecular loci associated with seed isoflavone content may underlie resistance to soybean pod borer (Leguminivora glycinivorella)

Soybean pod borer (SPB) (Leguminivora glycinivorella (Mats.) Obraztsov) causes severe loss of soybean (Glycine max L. Merr.) seed yield and quality in some regions of the world, especially in north‐eastern China, Japan and Russia. Isoflavones in soybean seed play a crucial role in plant resistance to diseases and pests. The aim of this study was to find whether SPB resistance QTL are associated with soybean seed isoflavone content. A cross was made between ‘Zhongdou 27’ (higher isoflavone content) and ‘Jiunong 20’ (lower isoflavone content). One hundred and twelve F_5:10 recombinant inbred lines were derived through single‐seed descent. A plastic‐net cabinet was used to cover the plants in early August, and thirty SPB moths per square metre were put in to infest the soybean green pods. The results indicated that the percentage of seeds damaged by SPB was positively correlated with glycitein content (GC), whereas it was negatively correlated with genistein (GT), daidzein (DZ) and total isoflavone content (TI). Four QTL underlying SPB damage to seeds were identified and the phenotypic variation for SPB resistance explained by the four QTL ranged from 2% to 14% on chromosomes Gm7, 10, 13 and 17. Moreover, eleven QTL underlying isoflavone content were identified, and ten of them were encompassed within the same four marker intervals as the SPB QTL (BARC‐Satt208‐Sat292, Satt144‐Sat074, Satt540‐Sat244 and Satt345‐Satt592). These QTL could be useful in marker‐assisted selection for breeding soybean cultivars with both SPB resistance and high seed isoflavone content.     

Inheritance of seed weight and growth habit in 10 intercross chickpea (Cicer arietinum) nested association mapping populations

Objective of investigation

Chickpea is a major global food legume for which seed weight and plant growth habit are important yield and harvestability components for plant breeding. This study tested seed weight and plant growth habit inheritance and identified quantitative trait loci (QTL).

Experimental material

A 10 nested association mapping (NAM) populations of chickpea were created from crosses between ‘Gokce’, a cultivar and wild crop relative accessions of Cicer reticulatum and Cicer echinospermum. Families were then developed to the F2:4 generation.

Method of investigation

A 10 families were grown at the Field Experiment Station, Harran University near Şanlıurfa, Turkey during 2019.

Data collection

A 100-seed weight and prostrate or erect growth habit was scored in the field. Two families were genotyped for 60 single-nucleotide polymorphisms (SNP).

Result and conclusions

A 100-seed weight showed polygenic control, and three QTLs were found. Growth habit was controlled by one or two QTLs. The two traits were significantly correlated for five populations. The crop wild relatives of chickpea contain variations at novel loci affecting seed weight compared to the literature.     

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.     

利用双向回交导入系定位水稻苗期耐亚铁毒和锌毒的QTL

铁和锌是水稻生长必需的微量元素,也是重金属污染元素。在低洼或酸性土壤中,水稻容易遭受亚铁和锌毒害,抑制水稻生长,造成生物量和产量下降。为探讨水稻苗期耐亚铁毒、锌毒的遗传机制,利用优质粳稻品种Lemont和高产籼稻品种特青为亲本构建的高代双向回交导入系和308个在染色体上均匀分布的SNP标记剖析耐亚铁毒、锌毒相关的QTL。从双向导入系共检测到42个影响耐亚铁毒、锌毒相关性状如苗高、苗干重、根干重以及胁迫与对照相对值的QTL,多数位点增强亚铁毒、锌毒抗性的有利等位基因来自Lemont。其中同时在2个背景下表达的QTL有4个,占定位QTL总数的9.52%,说明大多数QTL的表达具有明显的遗传背景效应。同一遗传背景下同时影响耐亚铁毒和锌毒的QTL有9个,其中QSdw5在2个背景中均被检测到,其效应大小和方向一致,说明水稻苗期耐亚铁毒、锌毒之间存在遗传重叠位点。因此,通过分子标记辅助选择从Lemont中导入或聚合有利的遗传重叠区域,可以提高特青对亚铁毒、锌毒的抗性水平。     

水稻基部伸长节间性状与倒伏相关性分析及QTL定位

利用珍汕97B/密阳46 RILs群体及其构建的连锁图谱，对水稻株高和基部Ⅰ、Ⅱ伸长节间性状与稻株抗倒伏能力进行相关分析，并对基部Ⅰ、Ⅱ伸长节间性状进行QTL定位，共检测到加性效应QTLs 16个、加性´加性互作33对。估算了每个QTL的加性效应值和每对加加互作的上位性效应值，比较了QTLs的基因组分布。在第1染色体短臂和第     

水稻株高QTL分析及其与产量QTL的关系

分别应用具有112和160个标记位点的两个籼/籼交组合的F2群体的连锁图,对控制水稻株高的数量性状基因(QTL)进行了研究.各定位了4个和3个株高QTL,每个QTL的贡献率在5.6%～22.9%之间.在一个群体中,4个QTL都表现为完全显性或超显性;在另一个群体中,3个QTL均表现为部分显性.分别检测到7对和5对影响株高的双基因互作,其中一个群体以     

Mapping of QTLs controlling epicotyl length in adzuki bean (Vigna angularis)

Epicotyl length (ECL) of adzuki bean (Vigna angularis) affects the efficiency of mechanized weeding and harvest. The present study investigated the genetic factors controlling ECL. An F₂ population derived from a cross between the breeding line ‘Tokei1121’ (T1121, long epicotyls) and the cultivar ‘Erimo167’ (common epicotyls) was phenotyped for ECL and genotyped using simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP) markers. A molecular linkage map was generated and fifty-two segregating markers, including 27 SSRs and 25 SNPs, were located on seven linkage groups (LGs) at a LOD threshold value of 3.0. Four quantitative trait loci (QTLs) for ECL, with LOD scores of 4.0, 3.4, 4.8 and 6.4, were identified on LGs 2, 4, 7 and 10, respectively; together, these four QTLs accounted for 49.3% of the phenotypic variance. The segregation patterns observed in F₅ residual heterozygous lines at qECL10 revealed that a single recessive gene derived from T1121 contributed to the longer ECL phenotype. Using five insertion and deletion markers, this gene was fine mapped to a ~255 kb region near the end of LG10. These findings will facilitate marker-assisted selection for breeding in the adzuki bean and contribute to an understanding of the mechanisms associated with epicotyl elongation.     

Dissection of genetic effects of quantitative trait loci (QTL) in transgenic cotton

When alien DNA inserts into the cotton genome in a multicopy manner, several quantitative trait loci (QTLs) in the cotton genome are disrupted; these are called dQTL in this study. A transgenic mutant line is near-isogenic to its recipient, which is divergent for the dQTL from the remaining QTLs. Therefore, a set of data from a transgenic QTL line mutated by Agrobacterium-mediated transformation (30074), its recipient and their F1 hybrids, and three elite lines were analyzed under a modified additive-dominance model with genotype × environment interactions in three different environments to separate the genetic effects due to dQTL from whole-genome effects. Our result showed that dQTL had significant additive effects on lint percentage, boll weight, and boll number per square meter, while it had little genetic association with fiber traits, seed cotton yield, and lint yield. The dQTL in 30074 significantly increased lint percentage and boll number, while significantly decreasing boll weight, having little effect on fibre traits, while those from the recipient and three elite lines showed significant genetic effects on lint percentage. In addition, the remaining QTL other than dQTL had significant additive effects on seed cotton yield, fruiting branch number, uniformity index, micronaire, and short fibre index, and significant dominance effects on seed cotton yield, lint yield, and boll number per square meter. The additive and dominance effects under homozygous and heterozygous conditions for each line are also predicted in this study.     

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.     

水稻萌发耐淹性种质资源筛选及QTL定位

萌发耐淹性种质资源的筛选、耐低氧萌发基因的挖掘和利用是选育适宜直播水稻新品种的基础。为简便、高效的评价种质资源的萌发耐淹性,本研究对来自不同年代和地区的191份粳稻种质资源进行了萌发耐淹性鉴定,共获得12份萌发耐淹性强的种质资源,其中连粳15号表现出较强的低氧萌发能力。利用其与籼稻品种黄莉占构建的F2:3分离群体,采用模拟大田的鉴定方法,在水稻1号、3号、9号、10号染色体上共检测到4个QTL,即qGS1、qGS3、qGS9和qGS10。共解释表型变异的70.9%,其中qGS1、qGS3和qGS10,能够被重复检测到,贡献率分别为19.2%~24.0%、12.6%~14.7%、19.1%~20.5%,是稳定表达的QTL位点。这些种质资源和QTL的发现为耐低氧发芽水稻新品种的培育提供了重要的亲本资源、基因资源和标记资源,同时也为选育优良直播稻品种提供了理论依据。     

Mapping of QTL controlling NIR predicted hot water extract and grain nitrogen content in a spring barley cross using marker-regression

A restriction fragment length polymorphism (RFLP) map constructed from 99 doubled haploid lines of a cross between two spring barley varieties (‘;Blenheim’בKym’) was used to map QTL controlling hot water extract and grain nitrogen content (predicted by analysis with near-infrared reflectance spectroscopy). Eight QTL affecting predicted hot water extract were identified by a marker-regression approach. The largest effects were found on chromosomes 3HL, associated with the denso dwarfing gene which is present in‘Blenheim’and conferred poorer predicted hot water extract quality, and 4HL. Other QTL were detected on chromosomes IHS. IHL. 2HS, 2HL. 5HL and 6HS. Analysis of single markers by analysis of variance detected an additional effect on chromosome 1H. Eight QTL affecting predicted grain nitrogen content were identified by marker-regression, on chromosomes 1HS, 1HL. 2HL. 5HS, 6H, 7HS and 7HL. There was also evidence for an additional QTL on chromosome 5HL. The positions of the grain nitrogen content QTL on 5HS and 5HL are comparable to QTL on wheat chromosomes 5A and 5D that affect grain protein content. The denso gene had no detectable effect on grain nitrogen content.     

利用大豆分子连锁图定位大豆孢囊线虫4号生理小种抗性QTL

大豆孢囊线虫 (SCN ,HeteroderaglycinesIchinohe)是一种土传的定居性内寄生线虫 ,是引起大豆黄萎病的病原 ,是大豆生产上危害最大的病害之一。SCN的生理小种多达十几种 ,在我国大豆孢囊线虫病原主要为 4号生理小种 ,它是现有生理小种中致病力最强的小种。经典遗传学研究已经确定大豆孢囊线虫抗性基因由 1- 4对核基因控制 ,估计有 10个以上的抗性座位。近年来分子标记技术及QTL定位方法的发展为深入研究该病害的抗性遗传规律提供了有效的手段 ,这对加速我国抗大豆抗孢囊线虫新品种培育具有重要意义。本研究以晋豆 2 3×ZDD2 315组合F2 群体 (2 5 3个单株 )为试验材料 ,其中灰布支黑豆 (ZDD2 315 )是我国山西省农家品种 ,对大豆孢囊线虫 4号生理小种表现为高抗。利用塑料钵柱法进行SCN抗性鉴定 ,构建大豆孢囊线虫抗性主座位所在区域的分子图谱 ,并进行SCN的QTL定位及遗传效应分析。根据已发表的大豆A和G连锁群的分子遗传图谱 ,应用BSA法 ,获得了 8个与SCN4号生理小种抗性基因相关的SSR标记 ,它们是Satt0 38(176bp/ 182bp) ,Satt30 9(130bp/ 135bp) ,Satt6 10 (2 4 0bp/ 2 2 2bp) ,Sat_14 1(189bp/ 184bp) ,Satt187(30 0bp/ 2 5 0bp) ,Satt315 (2 5 3bp/ 2 4 8bp) ,Satt6 32 (2 86bp/ 2 90bp)和Sat_16 2(2     

棉花BC_5F_2代换系的产量及品质相关性状表型分析及QTL定位

本研究利用生产上推广的优良早熟陆地棉栽培品种中棉所36为受体亲本,海岛棉海1为供体亲本,选择培育了一套由303个单株组成的BC5F2代换系。从已构建的BC1F1遗传图谱上以5~10cM为标准挑选391对多态性标记进行分子检测,多数单株含有海岛棉代换片段数为2~10个。对该群体的单株产量、品质性状进行了表型鉴定,存在大量具有优良品质的单株,纤维强度最高的能达到37.8cN/tex,铃重、衣分、纤维长度、整齐度、马克隆值、伸长率及纤维强度超轮回亲本分别为17.82%、44.55%、46.86%、33.33%、74.92%、41.58%、42.57%。采用性状-标记间的单向方差分析,共定位了20个与产量性状和33个与纤维品质性状有关的QTL,其中qUN-14-2、qBW-2-20、qFL-2-20和qMV-1-38这4个QTL存在一定的遗传稳定性。鉴定的QTL大多是微效基因,解释表型变异为3.01%~9.69%,该研究为染色体单片段代换系的精细的分子研究奠定了基础。     

Localization of QTL for basal root thickness in <Emphasis Type="Italic">japonica</Emphasis> rice and effect of marker-assisted selection for a major QTL

Root traits are key components of plant adaptation to drought environment. By using a 120 recombined inbred lines (RILs) rice population derived from a cross between IRAT109, a japonica upland rice cultivar and Yuefu, a japonica lowland rice cultivar, a complete genetic linkage map with 201 molecular markers covering 1,833.8 cM was constructed and quantitative trait loci (QTLs) associated with basal root thickness (BRT) were identified. A major QTL, conferring thicker BRT, located on chromosome 4, designated brt4, explained phenotypic variance of 20.6%, was selected as target QTL to study the effects of marker-assisted selection (MAS) using two early segregating populations derived from crosses between IRAT109 and two lowland rice cultivars. The results showed that the flanking markers of brt4 were genetically stable in populations with different genetic backgrounds. In the two populations under upland conditions, the difference between the means of BRT of plants carrying positive and negative favorable alleles at brt4 flanking markers loci was significant. Phenotypic effects of BRT QTL brt4 were 5.05–8.16%. When selected plants for two generations were planted at Beijing and Hainan locations under upland conditions, MAS effects for BRT QTL brt4 were 4.56–18.56% and 15.46–26.52% respectively. The means of BRT for the homozygous plants were greater than that of heterozygous plants. This major QTL might be useful for rice drought tolerance breeding. L. Liu and P. Mu are contributed equally to this work.     

利用Mudgo/武育粳3号F2群体分析水稻抗灰飞虱QTL

灰飞虱是我国水稻生产上的重要害虫。Mudgo是一个高抗灰飞虱的籼稻品种,对灰飞虱具有强的排驱性和抗生性抗性。利用Mudgo/武育粳3号F₂群体,构建了含有177个单株的F₂群体的遗传连锁图谱。该连锁图包含104个SSR标记和3个Indel标记,覆盖整个水稻基因组1 409.9 cM,每两个标记之间的平均距离为13.2 cM。采用改进的苗期集团筛选法对177个F_2:3家系进行了抗性鉴定,通过Windows QTL Cartographer 2.5进行复合区间作图分析,在第2、3、12染色体上分别检测到抗灰飞虱QTL Qsbph2b、Qsbph3d和Qsbph12a,分别位于标记RM5791~RM29、RM3199~RM5442和I12-17~RM333 1之间,单个LOD值分别为3.25、3.11和6.82,贡献率分别为17.3%、15.6%和35.8%,各QTL增强抗性的等位基因效应均来自Mudgo。其中Qsbph12a与标记RM3331和I12-17紧密连锁。结合表型鉴定的结果,Qsbph12a应为抗灰飞虱主效QTL,与该位点紧密连锁的标记可用于抗灰飞虱快速选择辅助育种。     

Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa) through single‐segment substitution lines

Panicle length (PL), an important yield‐related trait, strongly affects yield components, such as grain number, grain density and rice quality. More than 200 panicle length quantitative trait loci (PL QTLs) are identified, but only a small number are applied in rice breeding. In this study, we performed QTL analysis for PL using 42 single‐segment substitution lines (SSSLs) derived from nine donors in the genetic background of HJX74. Fourteen QTLs and five heterosis QTLs (HQTLs) for PL were recognised. Three QTLs and four HQTLs acted positively, and the other eleven QTLs and one HQTL acted negatively. By scanning the single heterozygous background region of the F₂ population with large‐genetic‐effect SSSLs, we mapped PL loci qPL6‐2 and qPL7‐1 to different locations on chromosomes 6 and 7, respectively, in three consecutive years of independent trials. The genetic effects of these QTLs were further assessed. qPL6‐2 demonstrated the most positive additive effect (QTL), whereas qPL7‐1 achieved the most positive dominant effect (HQTL) for PL. These results indicated that the pyramiding of PL QTLs might increase grain yield and facilitate the application of the beneficial allele in hybrid rice breeding.     

Identification and mapping of a quantitative trait locus controlling extreme late bolting in Chinese cabbage (Brassica rapa L. ssp. pekinensis syn. campestris L.) using bulked segregant analysis

DNA markers linked to a locus controlling an extreme late bolting trait, which was originally found in a local cultivar of a non-heading leafy vegetable,‘Osaka Shirona Bansei’ (Brassica rapa L. ssp. pekinensis syn. campestris L.) were identified using bulked segregant analysis. A doubled haploid (DH) line, DH27, which is a progeny of ‘Osaka Shirona Bansei’, shows extreme late bolting, and bolts without vernalization. DH27 was crossed with a normal bolting DH line, G309. The plantlets of the parents, F₁ and F₂, were vernalized and then grown in a greenhouse. The bolting time of F₂ plants showed a continuous distribution from 19 to 231 days after vernalization (DAV), suggesting the effects of a few major genes and polygenes. Possible linkage markers for this trait were screened by modified bulked segregant analysis (BSA). The BSA using four bulks suggested that a 530-bp RAPD band RA1255C was linked to a locus controlling the bolting trait. The RAPD band was cloned and used as a probe to detect RFLP. The fragment detected a single locus, BN007-1,the segregation of which in the F₂ population matched that of RA1255C. Three other RAPDs were found to be linked to BN007-1. A quantitative trait locus(QTL) affecting the bolting time was detected around BN007-1 using MAPMAKER/QTL. Since the difference between bolting times of both the parental genotypes in the F₂ was 138 days, these markers may be useful for a marker-assisted selection (MAS) in the breeding program for late bolting or bolting-resistant cultivars in B. rapa crops. This revised version was published online in July 2006 with corrections to the Cover Date.     

不同环境条件下稻米组氨酸和精氨酸的胚乳和母体植株QTL分析

利用汕优63重组自交系与双亲回交产生的BC1F1和BC2F1群体,采用新发展的包括环境互作效应在内的多遗传体系QTL作图方法和基因定位软件,对稻米两种半必需氨基酸（组氨酸和精氨酸）进行三倍体胚乳和二倍体母体植株等不同遗传体系的QTL定位分析。共检测到10个控制组氨酸含量的QTL以及8个控制精氨酸含量的QTL。全部QTL均具有极显著的三倍体胚乳和二倍体母体植株基因的加性主效应,其中4个QTL具有显著或极显著的三倍体胚乳显性主效应,7个QTL还具有明显的环境互作效应。     

Mapping quantitative trait loci controlling soybean seed starch content in an interspecific cross of ‘Williams 82’ (Glycine max) and ‘PI 366121’ (Glycine soja)

Seed starch content (SSC) greatly affects the taste, flavour and processing properties of soy foods. The objective in this study was to identify quantitative trait loci (QTL) for SSC in soybean. A total in 169 recombinant inbred lines (RILs) derived from a cross in ‘Williams 82’ and ‘PI 366121’ were grown for three consecutive years. The SSC of the RILs displayed continuous variation with transgressive segregation and hence amenable for QTL mapping. Nine significant QTL exhibiting 5.6–11.3% of the total phenotypic variation (PVE) were identified. The QTL qSTR06_2 showed highest PVE (9.1–11.3%) at LOD values of 4.25–5.39. No stable QTL over 3 years were identified, indicating strong environmental influence on SSC. The QTL qSTR11_1 and qSTR20_1 were found to colocalize with some of the previously reported QTL for sucrose content in soybean, implying the interrelationship between starch and sucrose biosynthesis. As the carbohydrate components may affect key constituents such as oil and protein in soybean seed, findings of the study may be useful in breeding soybeans with improved seed composition.