Genetic analysis of plant height using two immortalized populations of “CRI12 × J8891” in Gossypium hirsutum L.

Plant height is an important plant architecture trait that determines the canopy structure, photosynthetic capacity and lodging resistance of upland cotton populations. To understand the genetic basis of plant height for marker-assisted breeding, quantitative trait loci (QTL) analysis was conducted based on the genetic map of recombinant inbred lines (RILs) derived from the cross “CRI12 × J8891” (Gossypium hirsutum L.). Three methods, including composite interval mapping, multiple interval mapping and multi-marker joint analysis, were used to detect QTL across multiple environments in the RILs and in the immortalized F₂ population developed through intermating between RILs. A total of 19 QTL with genetic main effects and/or genetic × environment interaction effects were identified on 15 chromosomes or linkage groups, each explaining 5.8–14.3 % of the phenotypic variation. Five digenic epistatic QTL pairs, mainly involving additive × additive and/or dominance × dominance, were detected in different environments. Seven out of eight interacting loci were main-effect QTL, suggesting that these loci act as major genes as well as modifying genes in the expression of plant height. The results demonstrate that additive effects, dominance and epistasis are all important for the genetic constitution of plant height, with additive effects playing a more important role in reducing plant height. QTL showing stability across environments that were repeatedly detected by different methods can be used in marker-assisted breeding.     

Identification of QTL underlying the filling rate of protein at different developmental stages of soybean seed

Seed protein content at the harvest stage is the sum of protein accumulation during seed filling. The aim of our investigation was to identify loci underlying the filling rate of seed protein at different developmental stages. To this end, we used 143 recombinant inbred lines (RILs) derived from the cross of soybean cultivars ‘Charleston’ and ‘Dongnong 594’ and composite interval mapping with a mixed genetic model. The genotype × environment interactions of the quantitative trait loci (QTL) were also evaluated. Thirty-nine unconditional QTL underlying the filling rate of seed protein at five developmental stages were mapped onto 14 linkage groups. The proportion of phenotypic variation explained by these QTL ranged from 4.88 to 26.05%. Thirty-eight conditional QTL underlying the filling rate of seed protein were mapped onto 16 linkage groups. The proportion of phenotypic variation explained by these QTL ranged from 1.87 to 31.34%. The numbers and types of QTL and their genetic effects on the filling rate of seed protein were different at each developmental stage. A G × E interaction effect was observed for some QTL.     

利用重组自交系定位棉花第22染色体短臂的纤维品质性状的QTL

 以TM-1的染色体片段代换系CSB22sh和TM-1杂交,构建了包含104个家系的重组自交系（RILs）群体。利用74对具有多态性位点的引物进行检测,构建了包含61个多态性位点,长度为76.93 cM的遗传图谱,平均标记间距离1.26 cM。利用此遗传图谱结合重组自交系群体4个环境下的5个纤维品质性状进行QTL定位,共定位出12个QTLs,解释性状表型变异的2.45%～21.11%;在1,2,3,4个环境中同时检测到的QTLs分别有9,1,1,1个。而利用4个环境平均值进行联合分析定位出个4个QTLs,纤维长度和纤维整齐度的QTLs均为2个,解释性状表型变异的14.37%～19.97%,并且纤维长度和整齐度的QTL在相同的位置。多环境下检测到的QTL可能对标记辅助选择有实际应用价值。     

Molecular mapping of quantitative trait loci for domestication traits and β-glucan content in a wheat recombinant inbred line population

Genetic maps are useful for analysis of quantitative trait loci (QTLs) and for marker-assisted selection (MAS) in breeding. A simple sequence repeat (SSR) marker linkage map of common wheat was constructed based on recombination inbred lines (RILs) derived from a cross between Chinese Spring and spelt wheat. The map included 264 loci on all wheat chromosomes covering 2,345.2 cM with 962, 794.6, and 588.6 cM for the A, B, and D genomes, respectively. Using the RILs and the map, we detected 42 putative QTLs on 15 chromosomes for ear length, spikelet number, spike compactness, kernel length, kernel width, kernel height and β-glucan content. Each QTL explained 4–45% of the phenotypic variation. Five QTL cluster regions were detected on chromosomes 1A, 5AL, 2B, 2D, and 4D. The first QTLs for β-glucan content in wheat were identified on chromosomes 3A, 1B, 5B, and 6D.     

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.     

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。     

Comparison of QTLs mapped in RILs and their test-cross progenies of tropical maize for insect resistance and agronomic traits

Quantitative trait loci (QTL) affecting resistance to south-western corn borer Diatraea grandiosella (SWCB) and sugarcane borer Diatraea saccharalis (SCB) have been identified previously in F_2:3 lines and recombinant inbred lines (RILs) of tropical maize using restriction fragment length polymorphism (RFLP) analyses. Our objective was to determine whether QTLs identified in these generations are also expressed in test crosses (TC) of RILs. A population of 166 TC progenies was developed by crossing RILs from the cross CML131 (susceptible) × CML67 (resistant) with the unrelated, susceptible tester line CML216. Resistance to first-generation SWCB, measured as leaf-feeding damage (LFD) under artificial infestation, and other agronomic traits were evaluated in two environments for the TC progenies and three environments for 183 RILs. The correlation between line per se and TC performance was low for LFD and intermediate for most agronomic traits. Estimates of the genotypic variance and heritabilities were smaller in the TC progenies than in the RILs for all traits. Quantitative trait loci were identified using an RFLP linkage map with 136 loci. For LFD, four QTLs were detected in the TC progenies, of which two were in common with nine QTLs previously mapped in the RILs. Few QTLs for agronomic traits were common to the two types of progeny, because of the low consistency of QTL positions for all traits in RIL and TC progenies, the use of TC progenies should be considered in QTL mapping studies as the first step for marker-assisted selection in hybrid breeding.     

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.     

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.     

Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100‐seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100‐seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17‐2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5‐1, qSW14‐1, qSW15‐1 and qSW15‐2, found to be the novel QTLs. A two‐dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.     

Mapping QTL for resistance to botrytis grey mould in chickpea

Botrytis grey mould (BGM) caused by Botrytis cinerea Pers. ex. Fr. is the second most important foliar disease of chickpea (Cicer arietinum L.) after ascochyta blight. An intraspecific linkage map of chickpea consisting of 144 markers assigned on 11 linkage groups was constructed from recombinant inbred lines (RILs) of a cross that involved a moderately resistant kabuli cultivar ICCV 2 and a highly susceptible desi cultivar JG 62. The length of the map obtained was 442.8 cM with an average interval length of 3.3 cM. Three quantitative trait loci (QTL) which together accounted for 43.6% of the variation for BGM resistance were identified and mapped on two linkage groups. QTL1 explained about 12.8% of the phenotypic variation for BGM resistance and was mapped on LG 6A. It was found tightly linked to markers SA14 and TS71rts36r at a LOD score of 3.7. QTL2 and QTL3 accounted for 9.5 and 48% of the phenotypic variation for BGM resistance, respectively, and were mapped on LG 3. QTL 2 was identified at LOD 2.7 and flanked by markers TA25 and TA144, positioned at 1 cM away from marker TA25. QTL3 was a strong QTL detected at LOD 17.7 and was flanked by TA159 at 12 cM distance on one side and TA118 at 4 cM distance on the other side. This is the first report on mapping of QTL for BGM resistance in chickpea. After proper validation, these QTL will be useful in marker-assisted pyramiding of BGM resistance in chickpea.     

A major QTL effect controlling resistance to powdery mildew in winter wheat at the adult plant stage

Powdery mildew is one of the major diseases of wheat in regions with a maritime or semi‐continental climate which can strongly affect grain yield. The objective of the study was to identify and compare quantitative resistance to powdery mildew of line RE9001 at the adult plant and vernalized seedling stages. RE9001 has no known Pm gene and shows a high level of adult plant resistance in the field. Using 104 recombinant inbred lines (RILs) of an RE9001 × ‘Courtot’ F8 population, a genetic map was developed with 363 markers distributed over 26 linkage groups and covering 3825 cM. The global map density was 1 locus/10.3 cM. RILs were assessed under field and tunnel greenhouse conditions for 2 years in two locations. Eleven quantitative trait loci (QTL) were detected at the adult stage and they explained 63% of the variation, depending on the environment. Three QTLs were found, at least, in the two environments. One QTL from RE9001, mapped on chromosome 2B, was stable in each environment. This QTL, QPm.inra.2B, explained 10.3–36.6% of the variation and could be mapped in the vicinity of the Pm6 gene. At the vernalized seedling stage, one QTL detected by the isolate 93‐27 could be an allele of the Pm3g gene present in ‘Courtot’. No residual effect of the Pm3g gene was detected at either stage. Markers flanking the QTL 2B could be useful tools to combine resistance to powdery mildew in wheat cultivars.     

Mapping QTL for seed yield and canning quality following processing of black bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Quantitative trait loci (QTL) analysis was conducted to identify QTL for seed yield and color retention following processing of a recombinant inbred line (RIL) black bean population. A population of 96 RILs were derived from the cross of black bean cultivars ‘Jaguar’ and 115M and evaluated in replicated trials at one location over 4 years (2004–2007) in Michigan. A 119-point genetic map constructed using simple sequence repeat (SSR), sequence related amplified polymorphism (SRAP), target region amplified polymorphism (TRAP) and phenotypic markers spanned fifteen linkage groups (LG) or 460 cM of the bean genome. Fourteen QTL for yield and color retention in four environments were identified by composite interval mapping on six linkage groups. A major QTL SY10.2^J115 for seed yield was identified on LG B10 with additional QTL on B3, B5, and B11. Color retention following processing was associated with loci on B1, B3, B5, B8, and B11. 115M possessed positive alleles for yield, but negative alleles for color retention. Some QTL for yield and color retention co-localized with regions identified in previous studies while others, particularly for color retention, were unique. Additional QTL for agronomic and canning quality traits were detected and individual contributions to future black bean breeding are discussed.     

栽培种花生荚果大小相关性状QTL定位

以远杂9102为母本,徐州68-4为父本杂交衍生的F5和F6共188个家系,构建了一张包含365个标记,总长度713.07 c M,标记间平均距离1.96 c M的栽培种花生遗传图谱。图谱包含22个连锁群,各连锁群平均长度12.37~81.39 c M,连锁群上标记数量3~46个。结合2013和2014年采集的荚果表型数据,采用Win QTLcart 2.5软件的复合区间作图法(composite interval mapping,CIM)进行QTL定位和效应估计。2个环境下共检测到41个QTL,其中与荚果长、宽、厚和百果重相关的QTL分别为13、7、13和8个,表型变异解释率为3.14%~18.27%。有6个QTL在2种环境下被重复检测到,其中百果重相关的2个(q HPWLG13.1、q HPWLG14.1),分布在LG13和LG14连锁群,遗传贡献率为6.95%~14.60%;与荚果长相关的3个(q LPLG2.2、q LPLG13.1、q LPLG14.1),分布在LG2、LG13和LG14连锁群,遗传贡献率为3.14%~18.27%;与荚果厚相关的1个(q TPLG3.4),分布在LG3连锁群,遗传贡献率为8.24%~9.24%。本研究涉及性状存在9个QTL热点区,每个热点区涉及2~3个性状,表型贡献率为3.57%~18.27%。     

Genomic regions associated with resistance to peanut bud necrosis disease (PBND) in a recombinant inbred line (RIL) population

Parents and 318 F₈ recombinant inbred lines (RILs) derived from the cross, TAG 24 × ICGV 86031 were evaluated for peanut bud necrosis disease (PBND) resistance and agronomic traits under natural infestation of thrips at a disease hotspot location for 2 years. Significant genotype, environment and genotype × environment interaction effects suggested role of environment in development and spread of the disease. Quantitative trait loci (QTL) analysis using QTL Cartographer identified a total of 14 QTL for six traits of which five QTL were for disease incidence. One quantitative trait locus q60DI located on LG_AhII was identified using both QTL Cartographer and QTL Network. Another QTL q90DI was detected with a high PVE of 12.57 using QTL Cartographer. A total of nine significant additive × additive (AA) interactions were detected for PBND disease incidence and yield traits with two and seven interactions displaying effects in favour of the parental and recombinant genotype combinations, respectively. This is the first attempt on QTL discovery associated with PBND resistance in peanut. Superior RILs identified in the study can be recycled or released as variety following further evaluations.     

Identification and mapping of a QTL for rachis internode length associated with cleistogamy in barley

General knowledge of the closed flowering trait, or cleistogamy, of barley is still limited. The relationship between cleistogamy and spike morphology characters was studied and linkage of cleistogamy genes with a highly significant quantitative trait locus (QTL) for rachis internode length on the long arm of chromosome 2H was detected. The mapping populations consisted of 129 doubled haploid lines of ‘Mikamo Golden’ × ‘Harrington’ and 150 F₂ plants of ‘Misato Golden’ × ‘Satsuki Nijo’. The phenotypic variance explained by this QTL accounted for 77.5% and 82.6% of the variance in rachis internode lengt, respectively, in these two populations. The peaks of the QTL coincided with the positions of the cleistogamy gene loci.     

Genome-wide QTL analysis for pre-harvest sprouting tolerance in bread wheat

A framework linkage map comprising 214 molecular marker (SSR, AFLP, SAMPL) loci was prepared using an intervarietal recombinant inbred line (RIL) mapping population of bread wheat. The RIL population that was developed from the cross SPR8198 (red-grained and PHS tolerant genotype) × HD2329 (white-grained and PHS susceptible genotype) following single seed descent segregated for pre-harvest sprouting (PHS). The RIL population and parental genotypes were evaluated in six different environments and the data on PHS were collected. Using the linkage map and PHS data, genome-wide single-locus and two-locus QTL analyses were conducted for PHS tolerance (PHST). Single-locus analysis following composite interval mapping (CIM) detected a total of seven QTL, located on specific arms of five different chromosome (1AS, 2AL, 2DL, 3AL and 3BL). These seven QTL included two major QTL one each on 2AL and 3AL. Two of these seven QTL were also detected following two-locus analysis, which resolved a total of four main-effect QTL (M-QTL), and 12 epistatic QTL (E-QTL), the latter involved in 7 QTL × QTL interactions. Interestingly, none of these M-QTL and E-QTL detected by two-locus analysis was involved in Q × E and Q × Q × E interactions, supporting the results of ANOVA, where genotype × environment interaction were non-significant. The QTL for PHS detected in the present study may be efficiently utilized for marker-aided selection for enhancing PHST in bread wheat.     

Identification of quantitative trait loci associated with resistance to foliar diseases in sorghum [<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench]

Forage sorghum cultivars grown in India are susceptible to various foliar diseases, of which anthracnose, rust, zonate leaf spot, drechslera leaf blight and target leaf spot cause severe damage. We report here the quantitative trait loci (QTLs) conferring resistance to these foliar diseases. QTL analysis was undertaken using 168 F₇ recombinant inbred lines (RILs) of a cross between a female parental line 296B (resistant) and a germplasm accession IS18551 (susceptible). RILs and parents were evaluated in replicated field trials in two environments. A total of twelve QTLs for five foliar diseases on three sorghum linkage groups (SBI-03, SBI-04 and SBI-06) were detected, accounting for 6.9–44.9% phenotypic variance. The morphological marker Plant color (Plcor) was associated with most of the QTL across years and locations. The QTL information generated in this study will aid in the transfer of foliar disease resistance into elite susceptible sorghum breeding lines through marker-assisted selection.