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.     

QTL mapping for capsaicin and dihydrocapsaicin content in a population of Capsicum annuum ‘NB1’ × Capsicum chinense ‘Bhut Jolokia’

Capsaicinoids are pungent compounds used for industrial and medical purposes including food, medicine and cosmetics. The Indian local variety ‘Bhut Jolokia’ (Capsicum chinense Jacq.) is one of the world's hottest chilli peppers. It produces more than one million Scoville heat units (SHUs) in total capsaicinoids. In this study, our goal was to identify quantitative trait loci (QTLs) responsible for the high content of capsaicin and dihydrocapsaicin in ‘Bhut Jolokia’. Capsicum annuum ‘NB1’, a Korean pepper inbred line containing 14 000 SHUs, was used as a maternal line. An F₂ population derived by crossing between ‘NB1’ and ‘Bhut Jolokia’ was generated to map QTLs for capsaicinoids content. A total of 234 markers, including 201 HRM, 21 SSR, 2 CAPS and 10 gene‐based markers of the capsaicinoid synthesis pathway, were mapped. The final map covered a total distance of 1175.2 cM and contained 12 linkage groups corresponding to the basic chromosome number of chilli pepper. Capsaicin and dihydrocapsaicin content were analysed in 175 F₂ pepper fruits using the HPLC method. The maximum total capsaicinoids content was 1389 mg per 100g DW (dry weight), and the minimum content was 11 mg per 100g DW. Two QTLs (qcap3.1 and qcap6.1) for capsaicin content were identified on LG3 and LG6, and two QTLs (qhdc2.1 and qdhc2.2) for dihydrocapsaicin content were located on LG2. We did not detect QTLs for total capsaicinoids content. The QTL positions for capsaicin content were different from those for dihydrocapsaicin content. These results indicate that the complexity of selecting for more pungent chilli peppers must be considered in a chilli pepper breeding programme. The QTL‐linked markers identified here will be helpful to develop more pungent pepper varieties from ‘Bhut Jolokia’, a very hot pepper.     

Fine mapping of a QTL for the number of spikelets per panicle by using near‐isogenic lines derived from an interspecific cross between Oryza sativa and Oryza minuta

We constructed a high‐resolution physical map for the qSPP7 QTL for spikelets per panicle (SPP) on rice chromosome 7 across a 28.6‐kb region containing four predicted genes. Using a series of BC₇F₄ near‐isogenic lines (NILs) derived from a cross between the Korean japonica cultivar ‘Hwaseongbyeo’ and Oryza minuta (IRGC Acc. No. 101144), three QTLs for the number of SPP, grains per panicle and primary branches were identified in the cluster (P ≤ 0.01). All three QTLs were additive, and alleles from the O. minuta parent were beneficial in the ‘Hwaseongbyeo’ background. qSPP7 was mapped to a 28.6‐kb region between the two simple sequence repeat (SSR) markers RM4952 and RM21605. The additive effect of the O. minuta allele at qSPP7 was 23 SPP, and 43.6% of the phenotypic variance was explained by the segregation of the SSR marker RM4952. Colocalization of the three QTLs suggested that this locus was associated with panicle structure and had pleiotropic effects. The NIL populations and molecular markers are useful for cloning qspp7.     

QTLs for black-point resistance in wheat and the identification of potential markers for use in breeding programmes

Quantitative trait loci (QTLs) for black‐point resistance have been mapped in two doubled haploid‐derived wheat populations, each thought to contain unrelated sources of resistance. In the ‘Sunco’בTasman’‐derived population, QTLs were located on chromosomes 1D, 2B, 3D, 4A, 5A and 7A with each QTL explaining between 4 and 15% of the observed phenotypic variance. QTLs were contributed by both parents. In the ‘Cascades’בAUS1408’‐derived population, QTLs from ‘Cascades’ were identified on chromosomes 2A, 2D and 7A with each QTL explaining between 12 and 18% of the phenotypic variance. Several markers were identified which are promising candidates for use in marker‐assisted selection programmes. If one, two or three of these markers would have been used to select for black‐point resistance in the ‘Sunco’בTasman’ population, then with one marker 34 of 39 resistant lines, with two markers 23 of 32 and with three markers 17 of 32 would have been selected. At the same time, 67 false positives obtained by selecting with one marker are reduced to 24 by selection with two markers and to 11 by selection with three markers. Similarly, if one, two or three markers are used to select for black‐point resistance in the ‘Cascades’בAUS1408’ populations, then with one marker 25 of 31 resistant lines, with two markers 26 of 31 and with three markers 10 of 31 are selected. At the same time, 14 false positives are obtained with one marker are reduced to six by selection with two markers and no false positives are selected using three markers.     

A novel aphid resistance locus in cowpea identified by combining SSR and SNP markers

The utility of combining simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) marker genotyping was determined for genetically mapping a novel aphid (Aphis craccivora) resistance locus in cowpea breeding line SARC 1‐57‐2 and for introgressing the resistance into elite cultivars by marker‐assisted backcrossing (MABC). The locus was tagged with codominant SSR marker CP 171F/172R with a recombination fraction of 5.91% in an F₂ population from ‘Apagbaala’ x SARC 1‐57‐2. A SNP‐genotyped biparental recombinant inbred line population was genotyped for CP 171F/172R, which was mapped to position 11.5 cM on linkage group (LG) 10 (physical position 30.514 Mb on chromosome Vu10). Using CP 171F/172R for foreground selection and a KASP‐SNP‐based marker panel for background selection in MABC, the resistance from SARC 1‐57‐2 was introduced into elite susceptible cultivar ‘Zaayura’. Five BC₄F₃ lines of improved ‘Zaayura’ that were isogenic except for the resistance locus region had phenotypes similar to SARC 1‐57‐2. This study identified a novel aphid resistance locus and demonstrated the effectiveness of integrating SSR and SNP markers for trait mapping and marker‐assisted breeding.     

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.     

Molecular mapping of a quantitative trait locus qSTV11Z harbouring rice stripe virus resistance gene,Stv‐b

Rice stripe virus (RSV) predominantly affects rice. In this study, we attempted to localize the quantitative trait locus (QTL) conferring RSV resistance in the ‘Zenith’ variety, which is known to harbour Stv‐a and Stv‐b. The resistant variety Zenith was crossed with the susceptible variety ‘Ilpum’ to generate a mapping population comprising 180 F_2:3 lines for QTL analysis. Contrary to previous findings, we could not detect Stv‐a‐specific QTLs on chromosome 6. Stv‐b‐specific QTL was detected on the long arm of chromosome 11; it was designated qSTV11^z. Six F_4:5 lines were selected from the F_3:4 population and fine‐mapped using insertion/deletion (InDel) markers. qSTV11^z was mapped to a 520‐kb region between the InDel markers Sid2 and Indel8. This region included OsSOT1 (candidate gene for STV11) and other previously reported RSV resistance QTLs. The OsSOT1 sequence in Ilpum and Zenith was identical to that of the susceptible variety ‘Koshihikari’, indicating that OsSOT1 is not the candidate gene of qSTV11^z. The localization of qSTV11^z should provide useful information for marker‐assisted selection and determination of genetic resources in rice breeding.     

Quantitative trait loci with additive and epistatic effects underlying resistance to two HG types of soybean cyst nematode

The resistance of soybean (Glycine max L. Merr.) cultivars varies with the different races of the soybean cyst nematode (SCN), Heterodera glycines, referred to as HG types (biotypes). Resistant cultivars with durable resistance are emphasized in recent years. The aim here was to identify quantitative trait loci (QTLs) for resistance to two SCN HG types (HG type 2.5.7, race 1; and HG type 1.2.3.5.7, race 4) in resistant cultivar ‘L‐10’ and to analyse the additive and epistatic effects of the identified QTLs. A total of 140 F₅‐derived F₁₀ recombinant inbred lines (F_5:10 RILs) were advanced via single‐seed‐descent from the cross between ‘L‐10’ (broadly resistant to SCN) and “Heinong 37” (SCN‐susceptible). For SCN HG type 2.5.7 and HG type 1.2.3.5.7 resistance, three and six QTLs for resistance to SCN HG type 2.5.7 and HG type 1.2.3.5.7 were identified, respectively, most of which could explain <10% of the phenotypic variation. Among these QTLs, five were identified over 2 years, while the other QTLs were detected in either 2009 or 2010. QSCN1‐2, located near the SSR marker Sat_069 of linkage group D1b (Chromosome, 2), was responsible for the largest proportion of phenotypic variation (16.01% in 2009 and 18.94% in 2010), suggested that it could effectively be used as a candidate QTL for the marker‐assisted selection (MAS) of soybean lines resistant to SCN. Additionally, for SCN HG type 2.5.7 and HG type 1.2.3.5.7 resistance, two and four QTLs showed an additive effect (a), respectively. One epistatic pair of QTLs (QSCN1‐1‐QSCN1‐3) for SCN HG type 2.5.7 resistance and eight epistatic pairs of QTLs for SCN HG type 1.2.3.5.7 resistance were found to have significant aa effects, among which one pair of QTLs (QSCN4‐4 and QSCN4‐5) contributed a large proportion of aa effects (3%). The results indicated that additive and epistatic effects could significantly affect SCN resistance. Therefore, both of a and aa effects should be considered in MAS programmes.     

Dissection of genetic variance of fibre quality in advanced generations from an interspecific cross of Gossypium hirsutum and G. barbadense

The interspecific genetic introgression approach has been shown to facilitate the detection and dissection of quantitative trait loci (QTL). A population consisting of 121 F₆ recombinant inbred lines was developed by crossing Gossypium hirsutum cv. ‘Handan 208’ and G. barbadense cv. ‘Pima 90’ via single‐seed descent. Genotyping indicated that the mean ‘Pima 90’ allele frequency at each locus was 21%. Phenotyping and phenotypic distribution indicated a trend of return of individual lines’ characters to ‘Handan 208’ coupled with a wide variance for each trait. Significant loci influencing fibre quality were detected by one‐way analysis of variance (anova; P < 0.005) and association analysis [?log₁₀(P) ≥ 3]: five and three markers for fibre length, four and one marker(s) for uniformity, two and one marker(s) for micronaire, 13 and 15 markers for strength, six and 10 markers for elongation, respectively. Two‐way anova based on genotypes of all marker loci combination showed that 807 two‐locus combinations were significant, and two‐way anova based on marker genotypes of QTL markers combination showed five significant digenic interactions (P < 0.01).     

Identification and marker‐assisted introgression of QTL conferring resistance to bacterial leaf blight in cowpea (Vigna unguiculata (L.) Walp.)

Bacterial leaf blight (BLB), caused by Xanthomonas axonopodis pv. vignicola (Xav), is widespread in major cowpea [Vigna unguiculata (L.) Walp.] growing regions of the world. Considering the resource poor nature of cowpea farmers, development and introduction of cultivars resistant to the disease is the best option. Identification of DNA markers and marker‐assisted selection will increase precision of breeding for resistance to diseases like bacterial leaf blight. Hence, an attempt was made to detect QTL for resistance to BLB using 194 F_2 : 3 progeny derived from the cross ‘C‐152’ (susceptible parent) × ‘V‐16’ (resistant parent). These progeny were screened for resistance to bacterial blight by the leaf inoculation method. Platykurtic distribution of per cent disease index scores indicated quantitative inheritance of resistance to bacterial leaf blight. A genetic map with 96 markers (79 SSR and 17 CISP) constructed from the 194 F₂ individuals was used to perform QTL analysis. Out of three major QTL identified, one was on LG 8 (qtlblb‐1) and two on LG 11 (qtlblb‐2 and qtlblb‐3). The PCR product generated by the primer VuMt337 encoded for RIN2‐like mRNA that positively regulate RPM1‐ and RPS2‐dependent hypersensitive response. The QTL qtlblb‐1 explained 30.58% phenotypic variation followed by qtlblb‐2 and qtlblb‐3 with 10.77% and 10.63%, respectively. The major QTL region on LG 8 was introgressed from cultivar V‐16 into the bacterial leaf blight susceptible variety C‐152 through marker‐assisted backcrossing (MABC).     

Development of molecular markers for crown rot resistance in wheat: mapping of QTLs for seedling resistance in a '2-49' × 'Janz' population

Crown rot, caused by Fusarium pseudograminearum, is an important disease of wheat in Australia and elsewhere. In order to identify molecular markers associated with partial seedling resistance to this disease, bulked segregant analysis and quantitative trait loci (QTL) mapping approaches were undertaken using a population of 145 doubled haploid lines constructed from ‘2‐49’ (partially resistant) × ‘Janz’ (susceptible) parents. Phenotypic data indicated that the trait is quantitatively inherited. The largest QTLs were located on chromosomes 1D and 1A, and explained 21% and 9% of the phenotypic variance, respectively. Using the best markers associated with five QTLs identified by composite interval mapping, the combined effect of the QTLs explained 40.6% of the phenotypic variance. All resistance alleles were inherited from ‘2‐49’ with the exception of a QTL on 2B, which was inherited from ‘Janz’. A minor QTL on 4B was loosely linked (19.8 cM) to the Rht1 locus in repulsion. None of the QTLs identified in this study were located in the same region as resistance QTLs identified in other populations segregating for Fusarium head blight, caused by Fusarium graminearum.     

Molecular mapping of a new gene for resistance to frogeye leaf spot of soya bean in 'Peking'

Amplified fragment length polymorphism (AFLP) and microsatellite (simple sequence repeat, SSR) techniques were used to map the _RGSp_eking gene, which is resistant to most isolates of Cercospora sojina in the soya bean cultivar ‘Peking’. The mapping was conducted using a defined F₂ population derived from the cross of ‘Peking’(resistant) בLee’(susceptible). Of 64 EcoRI and MseI primer combinations, 30 produced polymorphisms between the two parents. The F₂ population, consisting of 116 individuals, was screened with the 30 AFLP primer pairs and three mapped SSR markers to detect markers possibly linked to Rcs_Peking. One AFLP marker amplified by primer pair E‐AAC/M‐CTA and one SSR marker Satt244 were identified to be linked to Res_Peking. The gene was located within a 2.1‐cM interval between markers AACCTA178 and Satt244, 1.1 cM from Satt244 and 1.0 cM from AACCTA178. Since the SSR markers Satt244 and Satt431 have been mapped to molecular linkage group (LG) J of soya bean, the Res_Peking resistance gene was putatively located on the LG J. This will provide soya bean breeders an opportunity to use these markers for marker‐assisted selection for frogeye leaf spot resistance in soya bean.     

Development of cleaved amplified polymorphic sequence (CAPS) markers linked to a green rice leafhopper resistance gene, Grh3(t)

The chromosomal location of the resistance gene for green rice leafhopper (GRLH), an injurious insect for rice, has been determined and RFLP markers closely linked to this gene have been identified. The susceptible japonica rice variety ‘Nipponbare’ was crossed with a resistant japonica rice line ‘Aichi42’, in which green rice leaf hopper resistance had been introduced from an indica variety ‘Rantaj‐emas2’, and the 100 F₂ plants obtained were used for linkage analysis. The green rice leafhopper resistance gene, Grh3(t), was mapped between RFLP markers C288B and C133A on chromosome 6 and co‐segregated with C81. Of the RFLP markers tightly linked to Grh3(t), C81 was converted to a SCAR marker and C133A to a cleaved amplified polymorphic sequence marker that could distinguish the heterozygous genotype to establish an effective marker‐aided selection system for the GRLH resistance gene.     

Breeding cowpea for resistance to Striga gesnerioides in the Nigerian dry savannas using marker‐assisted selection

Historically, conventional breeding has been the primary strategy used to develop a number of Striga‐resistant varieties currently grown in the Sahel of Western Africa. In this study, we have successfully developed and applied a marker‐assisted selection strategy that employs a single backcross programme to introgress Striga resistance into farmer preferred varieties of cowpea for the Nigeria savannas. In this strategy, we have introduced the Striga resistance gene from the donor parent IT97K‐499‐35 into an elite farmer preferred cowpea cultivar ‘Borno Brown’. The selected 47 BC₁F₂ populations confirmed the recombinants with desirable progeny having Striga resistance gene(s). The 28 lines selected in the BC₁F_2:4 generation with large seed size, brown seed coat colour and carrying marker alleles were evaluated in the field for resistance to Striga resistance. This led to the selection of a number of desirable improved lines that were immune to Striga having local genetic background with higher yield than those of their parents and standard varieties.     

QTL mapping for heading date,leaf area and chlorophyll content under cold and drought stress in two related recombinant inbred line populations (Japonica rice) and meta‐analysis

Rice is highly susceptible to drought and cold. The goal of this study was to identify the QTLs affecting the rice heading date (HD), leaf area (LA) and chlorophyll content (CC) under cold and drought stress. A total of twenty‐nine and thirty‐eight additive QTLs were detected from two crosses of ‘Dongnong422’/‘Kongyu131’ and ‘Xiaobaijingzi’/‘Kongyu131’, respectively. qHD1‐7‐1, qHD1‐7‐2, qHD1‐2‐1, qLA1‐7‐1, qLA1‐6‐3 and qCC1‐7‐1 show adaptive effects under cold treatment, while qHD2‐2‐3, qHD2‐2‐2, qLA2‐7‐3 and qCC2‐5‐1 were important for explaining the genetic mechanism during drought tolerance. Additionally, nine and five additive × environment interaction QTLs were detected for two RILs, respectively. RIL26 and RIL73 were two lines that are associated with cold and drought for HD. 339 QTLs related to HD, CC and LA of rice from database and our research were projected onto the genetic map. Nine cloned genes and nineteen homologous candidate genes related to HD, CC, cold tolerance and drought tolerance were mapped by meta‐analysis. These results lay the foundation for the fine mapping of QTLs related to HD, LA and CC for marker‐assisted selection.     

Mapping quantitative trait loci (QTLs) underlying seed vitamin E content in soybean with main,epistatic and QTL × environment effects

Soybean (Glycine max (L.) Merr.) seed contains small amounts of tocopherol, a non‐enzymatic antioxidant known as lipid‐soluble vitamin E (VE). Dietary VE contributes to a decreased risk of chronic diseases in humans and has several beneficial effects on resistance to stress in plants, and increasing VE content is an important breeding goal for increasing the nutritional value of soybean. In this study, quantitative trait loci (QTLs) underlying VE content with main, epistatic and QTL × environment effects were identified in a population of F_5 : 6 recombinant inbred lines from a cross between ‘Hefeng 25’ (a low‐VE cultivar) and ‘OAC Bayfield’ (a high‐VE cultivar). A total of 18 QTLs were detected that showed additive main effects (a) and/or additive × environment interaction effects (ae) in different environments. Moreover, 19 epistatic pairs of QTLs were found to be associated with α‐tocopherol (α‐Toc), γ‐tocopherol (γ‐Toc), δ‐tocopherol (δ‐Toc) and total VE (TE) contents. The QTLs identified in multienvironments could provide more information about QTL by environment interactions and could be useful for the marker‐assistant selection of soybean cultivars with high seed VE contents.     

QTL mapping of fruit nutritional and flavor components in tomato (<Emphasis Type="Italic">Solanum lycopersicum</Emphasis>) using genome-wide SSR markers and recombinant inbred lines (RILs) from an intra-specific cross

Fruit nutritional and flavor components are important targets for breeding new cultivars of tomato (Solanum lycopersicum L.). We developed 108 recombinant inbred lines (the K39 RILs) in the F₆ generation from a cross between two phenotypically different breeding lines, K03 and K09. A linkage map was constructed using 172 genome-wide simple sequence repeat markers, 3 single-nucleotide polymorphism markers, and 2 phenotypic markers. The K39 RIL map consists of 12 linkage groups (LGs) and covers a genetic distance of 1089 cM. We measured the fruit soluble solids content (SSC), titratable acidity (TA), glutamic acid content (GLU), and lycopene content (LYC) of each line in four generations (F₆, F₈, F₁₀, F₁₁), β-carotene content (CAR) in two generations, and pH in one generation. By composite interval mapping that considered yearly variations in components as non-genetic effects, we detected three quantitative trait loci (QTLs) for SSC, four for TA, two for CAR, and one each for GLU, LYC, and pH. Among them, we found two QTLs for TA in LGs 6 and 11, those for GLU and LYC were candidates for novel QTLs. QTLs detected in this study were clustered in five LGs, but we observed no apparent trade-off relationships among the QTLs in each LG. Being derived from an intra-specific cross of tomato breeding materials, these QTLs can be used in practical breeding for improving fruit quality with low risk of linkage drag.     

Identification of marker alleles linked to fire blight resistance QTLs in apple genotypes

Molecular marker analysis can be an effective tool when searching for new fire blight resistance donors. It can speed up the breeding process as well, even though many of the available markers linked to fire blight resistance QTLs have not yet been tested by screening a large number of cultivars. The aim of this study was to search for alternate sources of the three major QTLs of fire blight resistance; FBF7, FB_MR5 and FB_E, as well as to test the efficiency of some markers linked to minor QTLs. Altogether, nine primer pairs were used on 77 genotypes including new Hungarian cultivars and old apple cultivars from the Carpathian basin. Several marker alleles of FB resistance QTLs have been detected in the screened genotypes, most importantly the alleles coupling with FB_MR5 in the old cultivars ‘Kéresi muskotály’, ‘Szabadkai szercsika’ and ‘Batul’. We propose these cultivars as the first available resistance donors of FB_MR5 instead of the crabapple Malus × robusta 5. The results also bring new information regarding the resistance alleles of new Hungarian cultivars and selections.     

Meta‐analysis and overview analysis of quantitative trait locis associated with fatty acid content in soybean for candidate gene mining

As soybean seed fatty acid content is valued in food, animal feed and some industrial applications, plant breeders continually aim to improve seed fatty acid constituent value. This study analysed 163 original quantitative trait loci (QTLs) related to soybean fatty acid content from databases and references and revealed 43 consensus QTLs. Meta‐analysis using BioMercator ver.2.1 indicated that these were located across 16 linkage groups (LGs) excluding LG D1a, LG C1, LG M and LG H. Moreover, the overview method was used to optimize these QTLs based on statistical analysis. Some valid QTL regions were narrowed down to 0.5 Mb and mapped on the same LGs as the meta‐analysis result. Furthermore, the functions of all genes located in these consensus QTL intervals were predicted and eight candidate genes were identified. KEGG pathway analysis indicated that Glyma.13G127900 and Glyma.18G232000 were involved in the fatty acid synthesis metabolic (pathway ID ko00071, ko00062, ko01040). These results lay a foundation for fine mapping of QTLs related to fatty acid content and marker‐assisted breeding in soybean.     

Identification of a novel QTL for the number of spikelets per panicle using a cross between indica‐ and japonica‐type high‐yielding rice cultivars in Japan

Yield is a complex trait. To improve it, the accumulation of the favourable alleles of valuable genes is required for each yield‐related trait. In this study, we used two high‐yielding rice cultivars developed in Japan, indica‐type ‘Takanari’ and japonica‐type ‘Momiroman’, for a genetic analysis of the sink capacity‐related traits. An F₂ population showed transgressive segregation for the number of spikelets per panicle. Quantitative trait locus (QTL) analysis detected four QTLs for the trait. Two of the QTLs were most likely identical to previously cloned GN1a and APO1, and their Takanari alleles had positive effects. The Momiroman alleles of the other two QTLs had positive effects, and one of these QTLs was most likely identical to SPIKE/GPS. The QTL on the long arm of chromosome 3 appeared to be novel; it clustered with QTLs for grain length and days‐to‐heading. Substitution mapping revealed that the close linkage of QTLs caused the clustering. These results suggest that the combination of the favourable alleles of detected QTLs could lead to greater sink capacity than that of the parental cultivars.