Genetic mapping and QTL analysis of fruit and flower related traits in cucumber (Cucumis sativus L.) using recombinant inbred lines

A set of 224 recombinant inbred lines (RILs) derived from a narrow cross between two fresh eaten types (S94 (Northern China type) × S06 (Northern European type)) (Cucumis sativus L.) was used to construct a genetic linkage map. With the RILs a 257-point genetic map was constructed including 206 SRAPs, 22 SSRs, 25 SCARs, 1 STS, and three economically important morphological markers (small spines (ss), uniform immature fruit color (u), dull fruit skin (D)). The seven linkage groups covered 1005.9 cM with a mean marker interval of 3.9 cM. The ss locus was linked to D and u, and they were all on Linkage group 6. The RIL map contained a total of 51 sequence-specific markers, which made possible the comparison of molecular linkage maps developed in different laboratories. Using the F_6:7 derived families, a total of 78 QTLs were detected with relatively high LOD scores (2.9–84.4) for nine fruit-related traits (fruit weight, length, and diameter, fruit flesh thickness, seed-cavity diameter, fruit-stalk length, fruit pedicel length, length/diameter and length/stalk ratio) and three flower-related traits (first flower node, first female flower node and female flower ratios). Several sequence-anchor markers (CSWCT25, CS30, CMBR41, CS08 etc.) were closely linked with some QTLs for fruit weight, fruit length, fruit flesh thickness and sex expression, which can be used for the future marker-assisted selection to improve the fruit traits in cucumber breeding. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. X. J. Yuan and J. S. Pan contributed equally to this investigation.     

崇化大梨×新世纪梨F1代分子遗传图谱的构建及两个果实性状的QTL分析

利用崇化大梨×新世纪梨杂交得到的94株F1代实生苗为作图群体,应用mapmaker/exp 3.0软件构建了一张包括19个SSR标记,315个SRAP标记,合计335个标记分属于18个连锁群的遗传图谱,图谱总长度为1 300 cM,平均图距为3.9 cM。采用区间作图法检测到与果实发育期、果形指数两个果实性状相连锁的QTL位点7个,其中主效的QTL位点2个(LOD≥3.5),分别位于LG2和LG17连锁群。     

QTL mapping of seedling traits in cucumber using recombinant inbred lines

Seedling traits are important for development, flower bud differentiation, fruit production and fruit quality of cucumber (Cucumis sativus L.). In this study, 160 recombinant inbred lines (RILs), derived from crossing wild cucumber inbred line PI 183967 (C. sativus var. hardwickii) with ‘931’ northern China cultivated cucumber inbred line 931, were employed to identify quantitative trait loci (QTLs) of cotyledon length (Cl), cotyledon width (Cw), hypocotyl length (Hl), first true leaf length (Fll), first true leaf width (Flw), aboveground fresh biomass (Afb) and aboveground dry biomass (Adb) at seedling stage. A genetic map including 307 SSR markers was developed which spanned 993.3 cM, with an average genetic distance of 3.23 cM between adjacent markers. 36 QTLs associated with the seven traits were detected on chromosomes 1, 2, 3, 5 and 6 in four environments (spring and autumn of 2012 and 2013), explaining 6.1 to 23.6% of the observed phenotypic variations. Among the 36 QTLs, 21 were responsible for more than 10% of observed phenotypic variations. We obtained 2, 2, 1 and 3 QTL loci for the traits of Fll, Flw, Afw and Adw, respectively. In addition, genes in the genetic region spanned by SSR15321‐SSR07711 on chr. 5 may contribute to Flw, Afw and Adw.     

Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.)

A genetic linkage map with 70 loci (55 SSR, 12 AFLP and 3 morphological loci) was constructed using 117 F₂ plants obtained from a cross between two upland cotton cultivars Yumian 1 and T586, which have relatively high levels of DNA marker polymorphism and differ remarkably in fiber-related traits. The linkage map comprised of 20 linkage groups, covering 525 cM with an average distance of 7.5 cM between two markers, or approximately 11.8% of the recombination length of the cotton genome. The present genetic linkage map was used to identify and map the quantitative trait loci (QTLs) affecting lint percentage and fiber quality traits in 117 F_2:3 family lines. Sixteen QTLs for lint percentage and fiber quality traits were identified in six linkage groups by multiple interval mapping: four QTLs for lint percentage, two QTLs for fiber 2.5% span length, three QTLs for fiber length uniformity, three QTLs for fiber strength, two QTLs for fiber elongation and two QTLs for micronaire reading. The QTL controlling fiber-related traits were mainly additive, and meanwhile including dominant and overdominant. Several QTLs affecting different fiber-related traits were detected within the same chromosome region, suggesting that genes controlling fiber traits may be linked or the result of pleiotropy.     

Mapping genes for double podding and other morphological traits in chickpea

Seed traits are important considerations for improving yield and product quality of chickpea (Cicer arietinum L.). The purpose of this study was to construct an intraspecific genetic linkage map and determine map positions of genes that confer double podding and seed traits using a population of 76 F₁₀ derived recombinant inbred lines (RILs) from the cross of ‘ICCV-2’ (large seeds and single pods) × ‘JG-62’ (small seeds and double podded). We used 55 sequence-tagged microsatellite sites (STMS), 20 random amplified polymorphic DNAs (RAPDs), 3inter-simple sequence repeats (ISSR) and 2 phenotypic markers to develop a genetic map that comprised 14 linkage groups covering297.5 cM. The gene for double podding (s) was mapped to linkage group 6 and linked to Tr44 and Tr35 at a distance of7.8 cM and 11.5 cM, respectively. The major gene for pigmentation, C, was mapped to linkage group 8 and was loosely linked to Tr33 at a distance of 13.5 cM. Four QTLs for 100 seed weight (located on LG4 and LG9), seed number plant^-1 (LG4), days to 50% flower (LG3) were identified. This intraspecific map of cultivated chickpea is the first that includes genes for important morphological traits. Synteny relationships among STMS markers appeared to be conserved on six linkage groups when our map was compared to the interspecific map presented by Winter et al. (2000). This revised version was published online in August 2006 with corrections to the Cover Date.     

大豆重组自交系群体NJRIKY遗传图谱的加密及其应用效果

作物基因组研究,包括基因或数量性状位点(QTL)定位、图位克隆以及物理图谱构建等,首先必须建立具有丰富标记信息的高密度遗传连锁图谱。由科丰1号和南农1138-2杂交组合衍生的重组自交系群体NJRIKY已经构建了4张大豆遗传连锁图谱,但由于遗传信息和标记数目不够充分,在基因和QTL作图时仍然存在精确度和准确度问题。为增加NJRIKY图谱密度,本研究在967对SSR引物中获得了401个多态性SSR标记。结合其他分子数据,使用作图软件Mapmaker/Exp3.0b,获得一张含有553个遗传标记,25个连锁群,总长2071.6cM,平均图距3.70cM的新遗传连锁图谱,其中SSR标记316个,RFLP标记197个,EST标记39个,形态标记1个。连锁群上大于20cM的标记间隔由原来42个减少到2个。原图谱的3个SMV抗性基因定位于D1b连锁群末端的开放区间上且仅与一个RFLP标记连锁,利用加密图谱对Rsc-3、Rsc-7、Rsc-9、Rsc-13、Rsa、Rn1和Rn3等7个SMV抗性基因重定位,全部位于D1b连锁群,与相邻分子标记距离均小于6cM,其中Rsc-9、Rn1、Rsa的距离小于1cM,Rsc-13与EST标记GMKF168a共分离。对本群体农艺性状进行QTL重定位,获得8个性状相关的42个主效QTL,其中20个QTL遗传贡献率大于10%,与原图谱比较,新定位的各QTL的标记区间明显缩短,与相邻标记的连锁更加紧密。     

Genetic mapping and QTL analysis for sugar yield-related traits in sugarcane

Genetic improvement of sugar content in sugarcane would benefit from the availability of sufficient DNA markers and a genetic map. Genetic linkage maps were constructed to identify quantitative trait loci (QTLs) for seedling brix (SB), brix (B), sucrose percent in juice (SUC), stalk number (SN), stalk length (SL), stalk diameter (SD), internodes (INT), number of green leaves (NGL), at three crop cycles across seven environments in a segregating population with 207 individuals derived from a bi-parental cross of sugarcane elite cultivars. Linkage analysis led to the construction of eight linkage groups (LGs) for Co86011 and sixteen LGs for CoH70. The combined length of the two linkage maps was 2606.77 cM distributed over 24 LGs. 31 QTLs were identified: 2 for SB, 7 for B, 6 for SUC, 4 for SN, 1 for SL, 3 for SD, 6 for INT and 2 for NGL at LOD scores ranging from 2.69 to 4.75. 7 QTLs (22 %) had stable effect across crop year and locations. Markers from parents were found to be associated with both positive and negative effect on all of the traits analyzed. The most important QTLs intervals identified in this study using single-dose marker, were qB2, qSUC2, qINT2 and qB2, qSUC2, qSL2, qINT2 located between SSR markers UGSM31₅₄₈ and UGSM31₆₄₉. These QTLs could be put into use in marker assisted breeding.     

烤烟6个农艺性状的QTL定位

由于烟草的分子标记开发和遗传图谱构建十分困难,迄今烟草中有关数量性状基因座(QTL)的定位研究仍非常有限。本研究利用一个由207个株系组成的烤烟DH群体及基于该群体所构建的含有24个连锁群、611个SSR标记,总长为1 882.1 cM的遗传图谱,采用复合区间作图方法,对株高(PH)、茎围(SG)、节距(IL)、叶片数(LN)、最大腰叶长(LWL)和最大腰叶宽(WWL) 6个与叶片产量有关的农艺性状进行QTL定位分析。共检测到69个QTL,大部分QTL的效应值较小,仅有4个具有较大的效应值,可解释大约15%~20%的表型变异。6个性状之间大多彼此相关。与此相符,在基因组中发现存在许多小区域,每个区域包含两个或两个以上紧密连锁的不同性状的QTL。     

Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton

Genetic mapping is an essential tool for cotton (Gossypium hirsutum L.) molecular breeding and application of DNA markers for cotton improvement. In this present study, we evaluated an RI population including 188 RI lines developed from 94 F₂-derived families and their two parental lines, ‘HS 46’ and ‘MARCABUCAG8US-1-88’, at Mississippi State, MS, for two years. Fourteen agronomic and fiber traits were measured. One hundred forty one (141) polymorphic SSR markers were screened for this population and 125 markers were used to construct a linkage map. Twenty six linkage groups were constructed, covering 125 SSR loci and 965 cM of overall map distance. Twenty four linkage groups (115 SSR loci) were assigned to specific chromosomes. Quantitative genetic analysis showed that the genotypic effects accounted for more than 20% of the phenotypic variation for all traits except fiber perimeter (18%). Fifty six QTLs (LOD > 3.0) associated with 14 agronomic and fiber traits were located on 17 chromosomes. One QTL associated with fiber elongation was located on linkage group LGU01. Nine chromosomes in sub-A genome harbored 27 QTLs with 10 associated with agronomic traits and 17 with fiber traits. Eight chromosomes in D sub-genome harbored 29 QTLs with 13 associated with agronomic traits and 16 with fiber traits. Chromosomes 3, 5, 12, 13, 14, 16, 20, and 26 harbor important QTLs for both yield and fiber quality compared to other chromosomes. Since this RI population was developed from an intraspecific cross within upland cotton, these QTLs should be useful for marker assisted selection for improving breeding efficiency in cotton line development. Paper number J1116 of the Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.     

Genetic mapping of QTLs for horticulture traits in a F2-3 population of bitter gourd (Momordica charantia L.)

An extensive genetic linkage map was constructed for bitter gourd (Momordica charantia L.) via the study of F₂ progenies derived from two cultivated inbred lines (gynoecia Z-1-4 and 189-4-1). The map included 194 loci on 11 chromosomes consisting of 26 EST-SSR loci, 28 SSR loci, 124 AFLP loci, and 16 SRAP loci. This map covered 1005.9 cM with 12 linkage groups. A total of 43 quantitative trait loci (QTLs), with a single QTL associated with 5.1–33.1 % phenotypic variance, were identified on nine chromosomes for 13 horticulture traits by analyzing the F_2-3 families and the genetic linkage map. The 13 horticulture traits which were investigated in three environments included female flower ratios (FFR), first female flower node (FFFN), fruit length, fruit diameter, flesh thickness, fruit shape, fruit pedicel length, fruit length pedicel ratios, fruit weight (FW), fruit numbers per plant (FPP), yield per plant (YPP), stem diameter (SD), and internodes length (IL). One QTL cluster region was detected on Lg-5 which contained the most important QTLs for YPP, FPP, FFFN, FFR, and FW with high contributions to phenotypic variance (5.8–25.4 %).     

Mapping and validation of QTLs for resistance to an Indian isolate of Ascochyta blight pathogen in chickpea

Ascochyta blight (AB) caused by Ascochyta rabiei, is globally the most important foliar disease that limits the productivity of chickpea (Cicer arietinum L.). An intraspecific linkage map of cultivated chickpea was constructed using an F₂ population derived from a cross between an AB susceptible parent ICC 4991 (Pb 7) and an AB resistant parent ICCV 04516. The resultant map consisted of 82 simple sequence repeat (SSR) markers and 2 expressed sequence tag (EST) markers covering 10 linkage groups, spanning a distance of 724.4 cM with an average marker density of 1 marker per 8.6 cM. Three quantitative trait loci (QTLs) were identified that contributed to resistance to an Indian isolate of AB, based on the seedling and adult plant reaction. QTL1 was mapped to LG3 linked to marker TR58 and explained 18.6% of the phenotypic variance (R ²) for AB resistance at the adult plant stage. QTL2 and QTL3 were both mapped to LG4 close to four SSR markers and accounted for 7.7% and 9.3%, respectively, of the total phenotypic variance for AB resistance at seedling stage. The SSR markers which flanked the AB QTLs were validated in a half-sib population derived from the same resistant parent ICCV 04516. Markers TA146 and TR20, linked to QTL2 were shown to be significantly associated with AB resistance at the seedling stage in this half-sib population. The markers linked to these QTLs can be utilized in marker-assisted breeding for AB resistance in chickpea.     

A genetic linkage map of Vigna vexillata

Vigna vexillata is a wild cross‐incompatible relative of cowpea. It is highly resistant to several diseases and pests plaguing cowpea. A linkage map was developed for V. vexillata comprising 120 markers, including 70 random amplified polymorphic DNAs, 47 amplified fragment length polymorphisms, one simple sequence repeat and two morphological traits namely, the cowpea mottle carmovirus resistance locus (CPMo V) and leaf shape (La), utilizing an F₂ generation of the intra‐specific cross Tvnu 1443’× Tvnu 73′. The genetic map comprised 14 linkage groups spanning 1564.1 cM of the genome. Thirty‐nine quantitative trait loci (QTLs) associated with nine traits were detected on the linkage map, explaining between 15.62 and 66.58% of their phenotypic variation. Seven chromosomal intervals contained QTLs with effects on multiple traits.     

Analysing genetic control of cooked grain traits and gelatinization temperature in a double haploid population of rice by quantitative trait loci mapping

Cooking quality in rice grains is a complex trait which requires improvement. Earlier reports show varying genetic influence on these traits, except for a common agreement on waxy (Wx) and alkali degeneration (Alk) loci on chromosome 6. The present study involved 86 doubled haploid lines derived from an indica × japonica cross involving IR64 and Azucena. Grain parameters viz., raw grain length (RGL), raw grain breadth (RGB), cooked grain length (CGL), cooked grain breadth (CGB), gelatinization temperature (GT), grain shape (RGS), length elongation ratio (LER) and breadth expansion ratio (BER) were subjected to mixed model mapping of quantitative trait loci (QTL). Segregation data of 175 markers covering a distance of 2395.5 cM spanning the entire genome were used. Fifteen main effect QTLs were detected spread over the genome, except on chromosomes 4, 8 and 11. Thirty epistatic interactions significantly influencing the traits were detected. Twelve of the main effect QTLs were involved in epistatic interactions. One main effect QTL associated with LER was detected near Alk locus. QTLs located for grain length on chromosomes 9 and 10 are reported for the first time. Detection of many epistatic loci and involvement of main effect QTLs in interactions demand for judicious selection of QTLs in marker-assisted selection programmes.     

陆地棉衣分差异群体产量及产量构成因素

 以衣分差异较大的陆地棉品种为材料,构建了包含188个F₂单株的作图群体,应用6111对SSR引物对亲本进行了分子标记筛选,结果仅获得了123个多态性位点,其中88个位点构建了总长为666.7 cM、平均距离为7.57 cM的遗传图谱,覆盖棉花基因组的14.9%。通过复合区间作图法对F₂单株和F_2∶3家系进行QTL检测,共鉴定出了18个控制产量及产量构成因素变异的QTLs,包括2个衣分QTLs、4个子棉产量QTLs、4个皮棉产量QTLs、2个衣指QTLs、3个单株铃数QTLs、2个铃重QTLs和1个子指QTL。 解释的表型变异分别为\{6.9%\}～16.9%、5.6%～16.2%、4.8%～15.6%、7.7%～13.3%、8.2%～11.6%、6.1%～7%和6.6%。不同QTLs在相同染色体区段上的成簇分布表明与产量性状相关的基因可能紧密连锁或一因多效。产量及产量构成因素QTLs的遗传方式主要以显性和超显性效应为主。检测到的主效QTLs可以用于棉花产量及产量构成因素的分子标记辅助选择。     

中棉所70分离群体农艺性状相关QTL定位

【目的】定位棉花产量相关性状的数量性状基因座(Quantitative trait locus,QTL)。【方法】以中棉所70的F_2分离群体为遗传作图群体,利用从14 820对简单序列重复(Simple sequence repeat,SSR)引物中筛选出的267对两亲本间的多态性引物检测F_2群体250个单株的标记基因型,利用Joinmap 4.0进行连锁分析,并通过WinQTLCart 2.5复合区间作图法对F_(2:3)群体的株高、单株结铃数和单株果枝数性状进行QTL定位。【结果】在F_2群体中共获得342个SSR标记位点,并构建了包括312个标记、35个连锁群,总长1 929.9 cM的遗传连锁图谱(标记间平均距离为9.2 cM,覆盖棉花基因组的43.4%)。经QTL定位,共检测到19个QTL,其中涉及株高的7个、单株果枝数4个、单株结铃数8个,这些QTL分布在8条染色体上,解释0.25%~11.28%的表型变异。【结论】这些与农艺性状相关的QTL有助于棉花产量分子标记辅助选择。     

栽培种花生遗传图谱的构建及主茎高和总分枝数QTL分析

栽培种花生是异源四倍体,基因组大,构建花生的分子遗传连锁图谱并对相关性状进行QTL定位研究的工作缓慢。本研究以遗传差异大的亲本组配杂交组合富川大花生×ICG6375构建F2作图群体,采用公开发表的2653对SSR引物,构建了一张含有234个SSR标记、分布于20个连锁群的栽培种花生遗传图谱。该图谱覆盖基因组的长度为1683.43c M,各个连锁群长度在36.11~131.48 c M之间,每个连锁群的标记数在6~15个之间,标记间的平均距离为7.19 c M。结合F3在湖北武汉和阳逻环境下的主茎高和总分枝数鉴定结果,应用Win QTLCart 2.5软件采用复合区间作图法进行了QTL定位和遗传效应分析。共检测到17个与主茎高和总分枝数相关的QTL位点,贡献率在0.10%~10.22%之间,分布于8个连锁群上。综合分析武汉和阳逻环境的鉴定结果,获得重复一致的与主茎高相关的6个QTL,其中q MHA061.1和q MHA062.1位于连锁群LG06上TC1A2~AHGS0153标记区间,贡献率为5.49%~8.95%;q MHA061.2和q MHA062.2位于LG06上AHGS1375~PM377标记区间,贡献率为2.93%~5.83%;q MHA092.2和q MHA091.1位于连锁群LG09上GM2839~EM87标记区间,贡献率为0.53%~9.43%。     

Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai)

Using an F₁ population from a cross between Japanese pear (Pyrus pyrifolia Nakai) cultivars ‘Akiakari’ and ‘Taihaku’, we performed quantitative trait locus (QTL) analysis of seven fruit traits (harvest time, fruit skin color, flesh firmness, fruit weight, acid content, total soluble solids content, and preharvest fruit drop). The constructed simple sequence repeat-based genetic linkage map of ‘Akiakari’ consisted of 208 loci and spanned 799 cM; that of ‘Taihaku’ consisted of 275 loci and spanned 1039 cM. Out of significant QTLs, two QTLs for harvest time, one for fruit skin color, and one for flesh firmness were stably detected in two successive years. The QTLs for harvest time were located at the bottom of linkage group (LG) Tai3 (nearest marker: BGA35) and at the top of LG Tai15 (nearest markers: PPACS2 and MEST050), in good accordance with results of genome-wide association study. The PPACS2 gene, a member of the ACC synthase gene family, may control harvest time, preharvest fruit drop, and fruit storage potential. One major QTL associated with fruit skin color was identified at the top of LG 8. QTLs identified in this study would be useful for marker-assisted selection in Japanese pear breeding programs.     

Identification of molecular markers linked to salt‐tolerant genes at germination stage of rice

An F_2 : 4 population derived from the cross between salt‐tolerant variety ‘Gharib’ (indica) and salt‐sensitive variety Sepidroud (indica) was used to determine the germination traits. The seeds were treated with 80 mm NaCl (salt stress), and 11 traits were determined as indicators for salt‐tolerant including germination rate, germination percentage, radicle length, plumule length, coleoptile length, plumule fresh and dry weight, radicle fresh and dry weight and coleoptile fresh and dry weight. A linkage map of 2475.7 cM with an average interval of 10.48 cM was constructed using 105 amplified fragment length polymorphism (AFLP) markers and 131 SSR markers. As many as that 17 quantitative trait loci (QTLs) were detected related to germination traits under salt stress condition; some of them are being reported for first time. Also, overlapping of QTLs related to salt tolerance was observed in this study. The identification of genomic regions associated with salt‐tolerant and its components under salt stress will be useful for marker‐based approaches to improve salt‐tolerant for farmers in salt‐prone rice environments.     

转基因抗虫棉产量相关性状QTL的分子标记及定位

 采用亚洲棉渐渗的纤维强度突出的陆地棉优质新品系0-153与陆地棉转基因抗虫新品系sGK9708为亲本,构建了F₂及F_2∶3分离群体。利用3869对SSR引物筛选亲本,得到125对多态性引物。进一步对183个F₂群体单株分析得到150个多态性标记位点,其中100个标记位点连锁,构建20个连锁群,共覆盖660 cM,占棉花总基因组的14.67%,每个连锁群平均包含5个标记位点,标记间平均相距6.6 cM,其中13个连锁群确定了对应的染色体。利用F₂和F_2:3数据,通过复合区间作图,共检测到28个产量及相关因素的QTLs。这些控制产量性状的QTLs只存在于5个连锁群上,成簇分布。与皮棉产量性状有关的2个QTLs,均与其它多个产量相关性状的QTLs在同一个连锁区段内,增效基因遗传效应方向一致,有必要研究其在标记辅助选择中的效果。本研究没有检测到在多世代表现稳定的QTL。因此,需要培育重组自交系,进一步明确产量性状有关QTL的遗传效应。