Marker-assisted selection of common beans for resistance to common bacterial blight: efficacy and economics

The possibility of using random amplified polymorphic DNA (RAPD) markers previously mapped in the common bean PC50/XANI59 population to select for resistance to common bacterial blight (CBB) in different populations was examined. Two out of 02 selected RAPD markers were polymorphic in HR56 and W0633d, the parental lines used in this experiment. Cosegregation analysis of the two polymorphic markers and disease reaction in a recombinant inbred (RI) population derived from HR67/W1744d confirmed that one of the two RAPD markers, BC420₉₀₀, was significantly associated with a major quantitative trait locus‐conditioning resistance to CBB in HR67. This locus accounted for approximately 51) of the phenotypic variation. The RAPD marker was transformed into a sequence characterized amplified region (SCAR) marker and used for selection in a different population derived from ‘Envoy’/HR67. Prediction for resistance to CBB with the BC420_.990 SCAR marker was 94.2% accurate in this population. A comparison between marker‐assisted selection (MAS) and conventional greenhouse screening showed that the cost of MAS is about one‐third less than that of the greenhouse test.     

Backcross breeding for improved resistance to common bacterial blight in pinto bean (Phaseolus vulgaris L.)

Common bacterial blight (CBB) caused by Xanthomonas campestris pv. phaseoli reduces common bean (Phaseolus vulgaris L.) yield and quality worldwide. Genetic resistance provides effective disease control; however. a high level of resistance is difficult to attain and does not exist in pinto bean, the most important dry bean market class in North America. Our objective was to determine if a backcross breeding approach with the aid of molecular markers linked to quantitative trait loci (QTL) for resistance to CBB in a donor parent could be used to attain higher levels of resistance to CBB in pinto bean. QTL conditioning CBB resistance from the donor parent XAN 159 were introgressed into the recurrent parent‘Chase’using classical backcross breeding and intermittent marker‐assisted selection.‘Chase’pinto bean is moderately resistant and the breeding line XAN 159 is highly resistant to Xanthomonas campestris. Marker assays confirmed the presence of independent QTL from GN no. 1 Sel 27 and XAN 159 in advanced backcross‐derived pinto bean lines with improved CBB resistance. Agronomic characteristics of‘Chase’were fully recovered in the backcross‐derived lines. An important QTL for CBB resistance from XAN 159 on linkage group B6 was not introgressed because tight linkage between this QTL and the dominant V allele that causes an unacceptable black‐mottled seed coat colour pattern in pinto bean could not be broken.     

DAF marker tightly linked to a major locus for Ascochyta blight resistance in chickpea (Cicer arietinum L.)

Resistance of chickpea against the disease caused by the ascomycete Ascochyta rabiei is encoded by two or three quantitative trait loci, QTL1, QTL2 and QTL3. A total of 94 recombinant inbred lines developed from a wide cross between a resistant chickpea line and a susceptible accession of Cicer reticulatum, a close relative of cultivated chickpea, was used to identify markers closely linked to QTL1 by DNA amplification fingerprinting in combination with bulked segregant analysis. Of 312 random 10mer oligonucleotides, 3 produced five polymorphic bands between the parents and bulks. Two of them were transferred to the population on which the recent genetic map of chickpea is based, and mapped to linkage group 4. These markers, OPS06-1 and OPS03-1, were linked at LOD-scores above 5 to markers UBC733B and UBC181A flanking the major ascochyta resistance locus. OPS06-1 mapped at the peak of the QTL between markers UBC733B (distance 4.1 cM) and UBC181A (distance 9.6 cM), while OPS03-1 mapped 25.1 cM away from marker UBC733B on the other flank of the resistance locus. STMS markers localised on this linkage group were transferred to the population segregating for ascochyta resistance. Three of these markers were closely linked to QTL1. Twelve of 14 STMS markers could be used in both populations. The order of STMS markers was essentially similar in both populations, with differences in map distances between them. The availability of flanking STMS markers for the major resistance locus QTL1 will help to elucidate the complex resistance against different Ascochyta pathotypes in future. This revised version was published online in August 2006 with corrections to the Cover Date.     

QTL mapping of a partial resistance to the corn delphacid‐transmitted viruses in Lepidopteran‐resistant maize line Mp705

A partial resistance to maize mosaic virus (MMV) and maize stripe virus (MStV) was mapped in a RILs population derived from a cross between lines MP705 (resistant) and B73 (susceptible). A genetic map constructed from 131 SSR markers spanned 1399 cM with an average distance of 9.6 cM. A total of 10 QTL were detected for resistance to MMV and MStV, using composite interval mapping. A major QTL explaining 34–41% of the phenotypic variance for early resistance to MMV was detected on chromosome 1. Another major QTL explaining up to 30% of the phenotypic variation for all traits of resistance to MStV was detected in the centromeric region of chromosome 3 (3.05 bin). After adding supplementary SSR markers, this region was found to correspond well to the one where a QTL of resistance to MStV already was located in a previous mapping study using an F₂ population derived from a cross between Rev81 and B73. These results suggested that these QTL of resistance to MStV detected on chromosome 3 could be allelic in maize genome.     

An SSR marker in the nitrate reductase gene of common bean is tightly linked to a major gene conferring resistance to common bacterial blight

A simple sequence repeat (SSR) marker composed of a tetra nucleotide repeat is tightly linked to a major gene of common bean (Phaseolus vulgaris L.) conferring resistance to common bacterial blight (CBB) incited by Xanthomonas axonopodis pv. phasoli (Xap). This SSR is located in the third intron region of the common bean nitrate reductase (NR) gene, which is mapped to linkage group (LG) H7, corresponding to LG B7 of the bean Core map. Co-segregation analysis between the SSR marker and CBB resistance in a recombinant inbred line (RIL) population demonstrated a tight linkage between the NR gene-specific marker and the major gene for CBB resistance. In total, the marker explained approximately 70% of the phenotypic variation in the population. Because it is co-dominant, this SSR marker should be more efficient for marker-assisted selection (MAS) than dominant/recessive random amplified polymorphic DNA (RAPD) or sequence characterized amplified region (SCAR) markers that have been developed, especially for early generation selection. This revised version was published online in August 2006 with corrections to the Cover Date.     

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.     

Interaction of common bacterial blight quantitative trait loci in a resistant inter‐cross population of common bean

Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli, is an important disease of common bean (Phaseolus vulgaris L.). Genetic resistance is the most economically efficient, environmentally friendly and socially acceptable approach to control plant diseases including CBB. To examine the main and interaction effects of the previously identified CBB resistance quantitative trait loci (QTL) associated with markers BC420 (B) on Pv06, SAP6 (S) on Pv10 and PVctt001 (P) on Pv04, in presence of the major QTL associated with the marker SU91 (S_u) on Pv08, a resistant F_4:5 recombinant inbred line population of the reciprocal crosses between OAC Rex (bb/ss/PP/S_uS_u) and HR45 (BB/SS/pp/S_uS_u) was evaluated under artificial field inoculation in disease nurseries in 2009 and 2010. While, in presence of the CBB QTL on Pv08, the QTL on Pv06 of HR45 accounted for 37–46% of phenotypic variation in the field, the effect of QTL on Pv04 and Pv10 were not significant under field conditions, even in the absence of the Pv06 QTL. Broad‐sense heritability estimates of CBB resistance and the QTL associated with BC420 were high for CBB severity and the area under the disease progress curve, promoting the continued efforts in pyramiding the QTL on Pv06 and Pv08 in common background, which provide high levels of resistance.     

Molecular markers linked to genes for specific rust resistance and indeterminate growth habit in common bean

Bulked segregant analysis was utilized to identify random amplified polymorphic DNA (RAPD) markers linked to genes for specific resistance to a rust pathotype and indeterminate growth habit in an F2 population from the common bean cross PC-50 (resistant to rust and determinate growth habit) × Chichara 83-109 (susceptible to rust and indeterminate growth habit). Six RAPD markers were mapped in a coupling phase linkage with the gene ( Ur-9) for specific rust resistance. The linkage group spanned a distance of 41 cM. A RAPD marker OA4.1050 was the most closely linked to the Ur-9 gene at a distance of 8.6 cM. Twenty-eight RAPD markers were mapped in a coupling phase linkage with the gene ( Fin) for indeterminate growth habit. The linkage group spanned a distance of 77 cM. RAPD markers OQ3.450 and OA17.600 were linked to the Fin allele as flanking markers at a distance of 1.2 cM and 3.8 cM, respectively. The RAPD markers linked to the gene for specific rust resistance of Andean origin detected here, along with other independent rust resistance genes from other germplasm, could be utilized to pyramid the different genes into a bean cultivar for durable rust resistance.     

来自野生二粒小麦的抗白粉病基因PmAS846及其染色体定位和分子标记分析

N9738是经抗性定向选择和农艺性状筛选所培育的抗白粉病普通小麦新种质,携带来自野生二粒小麦As846的抗白粉病基因PmAS846,在苗期和成株期高抗白粉菌生理小种E09和陕西关中地区流行菌系,本研究对该种质携带的抗白粉病基因进行了染色体定位和分子标记分析。对N9738和高感小麦白粉病的普通小麦品种辉县红杂交的F₁、F₂代分离群体和F_2:3代家系进行白粉病抗性鉴定和遗传分析证实,N9738苗期抗性由1个显性抗白粉病基因控制,单(缺)体分析将该基因定位在小麦5B染色体上。采用位于5B染色体的分子标记结合集群分离分析法(BSA法)分析,筛选出与PmAS846连锁的11个SSR标记和2个EST-STS标记,PmAS846两翼的SSR标记Xgwp3191和Xfcp1与该基因的遗传距离分别为7.3 cM和1.8 cM,EST-STS标记BF202652和BF482522与该基因的遗传距离均为5.1 cM。根据该基因两翼SSR标记对中国春5B染色体缺失系(Bin系)的分析将其定位在5B染色体长臂0.75~0.76区域。研究结果为PmAS846的分子标记辅助选择和精细定位奠定了基础。     

Genetic mapping for the Rf1 (fertility restoration) gene in sunflower (Helianthus annuus L.) by SSR and TRAP markers

The Rf1 gene in sunflower can effectively restore the pollen fertility of PET1 cytoplasm in male-sterile lines and has been widely used in commercial hybrid production. Identifying molecular markers tightly linked to this gene will be useful in marker-assisted selection to develop maintainer and restorer lines. Rf1 has been mapped to Linkage Group (LG) 13 of the public sunflower simple sequence repeat (SSR) map by aligning maps constructed from different populations and only one SSR marker was reported to be loosely linked to Rf1 . This paper reports the result of applying target region amplification polymorphism (TRAP) and SSR markers to map and develop a sequence-tagged site (STS) marker tightly linked to Rf1 using two populations derived from a cross between two U.S. public sunflower lines, RHA439 and cmsHA441. An SSR marker, ORS511, was 3.7 cM from the Rf1 gene and a TRAP marker, K11F05Sa12-160, was linked to Rf1 at a distance of 0.4 cM. This TRAP marker was converted to an STS marker for using in sunflower breeding.     

Genetic analysis of resistance to barley scald (Rhynchosporium secalis) in the Ethiopian line `Abyssinian' (CI668)

A doubled haploid barley (Hordeum vulgare L.) population from a cross between the cultivar `Ingrid' and the Ethiopian landrace `Abyssinian' was mapped by AFLP, RFLP, SSR and STS markers and tested for resistance to isolates`4004', `2', `16-6', `17', `22' and `WRS 1872' of Rhynchosporium secalis (Oudem.) J.J. Davis, the causal agent of leaf scald. Resistance tests were conducted on parents, DH-lines, a near-isogenic line of `Abyssinian' (NIL) into `Ingrid', and an F₂ population descended from the same F₁ plants as the DHs. The DH population segregated for at least two major R. secalis resistance QTL. All isolates tested identified a major QTL on chromosome 3 (3H) associated with R. secalis resistance, in a 4 cM support interval between the co-segregating markers Bmac0209/Falc666 and MWG680. The QTL was linked with the markers Falc666 (2.3 cM), YLM/ylp (0.3 cM), MWG680 (1.7 cM), cttaca2 (2.5 cM) and agtc17 (9.8 cM). The second QTL was located on chromosome 1 (7H).However, this QTL was only detected by one isolate and was located in an interval of 16 cM in the distal part of the chromosome. At this QTL the allele for improved scald resistance originated from the parent `Ingrid'. There were a number of minor QTL on chromosomes 2 (2H), 4 (4H) and 6 (6H) that were not repeatable either across replications or analysis methods. The importance of checking QTL-models by cross-validation is stressed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Stability of the association of molecular markers with common bacterial blight resistance in common bean (Phascolus vulgaris L.)

Common bacterial blight (CBB) caused hy Xanthomonas campestrts pv. phaseoli is an important disease of common bean (Phaseolus vulgaris L.) throughout the world. Two random amplified polymorphic DNA (RAPD) markers (R7313 and R4865) linked to genes for CBB resistance, that were transferred to P- vulgaris by an interspecific cross with Phaseohus acutifoluis. Were identified in a previous study. The current study was conducted to examine the use of these markers for selecting CBB resistant material from 85 F_5,6, lines derived from crosses between two of the resistant lines used previously in the linkage study and susceptible breeding lines. The results showed that these two markers were located on the same linkage group and explained 22% (P = 0.0002) of the variation in response to CBB in the current population. Seventy per cent of the lines that had both markers were classified as resistant in a disease test of the F_5,6, lines, whereas 73% of the lines that had neither of the RAPD markers were susceptible. The results indicated that the marker-disease resistance associations remained stable in a plant breeding programme and that they can be used lor marker-assisted selection of CBB-resistant beans.     

RFLP mapping of the three major genes, Vrn1, Q and B1, on the long arm of chromosome 5A of wheat

Chromosome 5A of wheat carries several major genes of agronomic importance, including Vrn1 controlling spring/winter wheat difference, Q determining spike morphology and B1 inhibiting awn development. A population of single-chromosome recombinant lines from the cross between two chromosome substitution lines, 'Chinese Spring' (Cappelle-Desprez 5A) and 'Chinese Spring' (Triticum spelta 5A) was developed to map these genes on the long arm of chromosome 5A relative to RFLP markers. Using 120 recombinant lines, a map of approximately 230 cM in length was constructed. The gene order was centromere– Vrn1– Q– B1. The Vrn1 locus was tightly linked to two RFLP markers, Xbcd450 and Xrz395 with 0.8 cM, and to Xpsr426 with 5.0 cM. The Vrn1-adjacent region was located in the central of the long arm, approximately 90 cM from the centromere. The chromosome region around Q and the 5A/4A translocation break-point were mapped by three RFLP markers, and their order was found to be Q– Xpsr370– Xcdo457–4A/5A break-point– Xpsr164. The B1 locus was located on the most distal portion of the long arm. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular mapping of genic male-sterile genes ms15, ms5 and ms6 in tetraploid cotton

Two genic male sterile (GMS) lines, Lang-A conditioned by ms ₁₅ and Zhongkang-A conditioned by ms ₅ ms ₆ duplicate recessive genes in Gossypium hirsutum L., were chosen to map GMS genes. These two lines were crossed with Gossypium barbadense cv. 'Hai7124' to produce segregating populations. The ms ₁₅ gene was mapped on chromosome 12, and was flanked by two simple sequence repeat (SSR) markers, NAU2176 and NAU1278, with a genetic distance of 0.8 and 1.9 cM respectively. The ms ₅ and ms ₆ genes were mapped to one pair of homoeologous chromosomes, ms ₅ on chromosome 12 flanked by three SSR markers, NAU3561, NAU2176 and NAU2096, with genetic distances of 1.4, 1.8 and 1.8 cM, respectively, and ms ₆ on chromosome 26 flanked by two SSR markers, BNL1227 and NAU460, with a genetic distance of 1.4 and 1.7 cM respectively. These tightly linked markers with the ms ₁₅ , ms ₅ and ms ₆ genes can be used in the marker-assisted selection among segregating populations in a breeding programme, and provide the foundation for gene isolation by map-based cloning for these three genes.     

青海大黄油菜粒色性状分子标记的开发和图谱整合

利用青海大黄油菜和褐籽白菜型油菜09A-126构建BC₄和F₂分离群体, 结合AFLP与群体分离分析法(bulked segregant analysis, BSA)筛选引物, 获得5个与黄籽基因Brsc1紧密连锁的分子标记Y11~Y15。5个AFLP特异片段的序列, 均与白菜型油菜的A9染色体部分序列表现同源。将5个AFLP标记成功转化为5个SCAR标记(SC11~SC15)。利用目标基因所在染色体区段序列筛选到7个与目标基因紧密连锁的SSR标记(BrID10607、KS10760、B089L03-3和A1~A4)。利用SCAR和SSR标记扫描F₂群体中部分单株, 发现SC14和A1为共显性标记。用BC₄群体将Brsc1定位在标记Y06和A4之间1.7 Mb的区间内, 遗传距离分别为0.115 cM和0.98 cM。标记Y05和Y12与Brsc1共分离。本研究为黄籽油菜分子标记辅助选择育种体系的建立及目标基因的进一步精细定位和图位克隆奠定了基础。     

YM型小麦温敏雄性不育系不育基因的QTL定位

YM型小麦温敏雄性不育系的不育基因被定位在1Bs染色体片段上, 但已发现的相邻分子标记与该基因的遗传距离较大, 达10 cM以上。为寻找与该基因连锁更紧密的分子标记, 以YM型温敏雄性不育系ATM3314与恢复系中国春杂交的F₂代200株为作图群体, 从1Bs的22个SSR引物中筛选出5个在亲本和F₂代中分离的SSR引物, 构建了1个包含5个标记的1Bs局部遗传连锁图谱。结合F₂代个体的育性调查, 采用复合区间作图法在YM型温敏雄性不育系的1Bs染色体上检测到不育基因的1个主效QTLrfv1-1和1个微效QTLrfv1-2。rfv1-1位于SSR标记Xgwm18和Xwmc406之间, 与两标记的遗传距离分别为6.0 cM和4.6 cM, LOD值为8.80, 加性效应23.87, 显性效应10.44, 可解释表型变异的23.91%; rfv1-2位于Xwmc406和Xbarc8之间, 与两标记的遗传距离分别为4.0 cM和3.4 cM, LOD值为3.10, 加性效应17.59, 显性效应5.99, 可解释表型变异的7.78%。本研究初步定位了YM型小麦温敏雄性不育系1Bs染色体片段上不育基因的QTL, 为进一步准确定位该基因奠定了基础。     

RAPD markers linked with restorer genes for the C-source of cytoplasmic male sterility in rye (Secale cereale L.)

The study was aimed at the identification of random amplified polymorphic DNA markers linked to genes controlling male sterility in rye with the C‐source of sterility‐inducing cytoplasm. Markers of male sterility were distinguished using bulk segregant analysis, carried out on the two F₂ crosses between male sterile and male fertile inbred lines. Screening of polymorphisms revealed by 1000 arbitrary 10‐mer primers allowed the detection of 10 markers in the cross between 711‐cmsC and DS2 lines and seven markers in the cross between 544‐cmsC and Ot0‐20 lines. Five markers were common for the two crosses, which allowed comparative mapping to be performed. Ten markers were mapped on the 4RL chromosome arm where two linked quantitative trait loci (QTL) for male sterility were discovered. Additional QTL of minor effect on male fertility were detected between the two linked markers provisionally assigned to the 6RS chromosome arm. The effectiveness of the marker‐assisted selection (MAS) for male‐sterile genotypes was evaluated.     

Using a linkage mapping approach to identify QTL for day-neutrality in the octoploid strawberry

A linkage mapping approach was used to identify quantitative trait loci (QTL) associated with day-neutrality in the commercial strawberry, Fragaria  ×  ananassa (Duch ex Rozier). Amplified Fragment Length Polymorphism (AFLP) markers were used to build a genetic map with a population of 127 lines developed by crossing the day-neutral (DN) 'Tribute' with the short-day (SD) 'Honeoye'. The population was genotyped with AFLP markers and 429 single dose restriction fragments (SDRF) were placed on a consensus map of 1541 cM with 43 linkage groups. Individuals from the mapping population were observed for their flowering habit throughout the growing season in Michigan (MI), Minnesota (MN), Maryland (MD), Oregon (OR) and California (CA). Eight QTL were found that were either location specific or shared among locations. None of these QTL explained >36% of the phenotypic variation, indicating that the inheritance of day-neutrality is likely a polygenic trait.     

绿豆遗传连锁图谱的整合

利用绿豆及其近缘种的701对SSR引物,对现有绿豆遗传连锁图谱进行补充,结果在高感豆象绿豆栽培种Berken和高抗豆象绿豆野生种ACC41两亲本间筛选到多态性SSR引物104对。群体分析后,结合其他分子数据,使用作图软件Mapmaker/Exp 3.0b,获得一张含有179个遗传标记和12个连锁群,总长1831.8cM、平均图距10.2cM的新遗传连锁图谱,包括97个SSR标记,91个来自绿豆近缘种;RFLP标记76个;RAPD标记4个;STS标记2个。对32个绿豆、小豆共用SSR标记在遗传连锁图谱的分布分析发现,二个基因组间有一定程度的同源性,共用标记在连锁群上的排列顺序基本上一致,只有部分标记显示绿豆和小豆基因组在进化过程中发生了染色体重排;利用新图谱对ACC41的抗绿豆象主效基因重新定位,仍定位于I(9)连锁群,与其相邻分子标记的距离均小于8cM,其中与右翼SSR标记C220的距离约2.7cM。与原图谱比较,新定位的抗性基因与其相邻标记的连锁更加紧密。     

RFLP-based mapping of the Sec-2 and Sec-5 loci encoding 75K γ-secalins of rye

For mapping the Sec2 and Sec5 loci of rye which determine expression of 75K γ-secalins, a partial genetic map of chromosome 2R spanning 64 cM was constructed. The map was developed using an F₂ population of 103 plants from a cross between two inbred lines. Both loci were mapped distally on the short arm of chromosome 2R and clearly tagged in relation to 12 restriction fragment length polymorphism (RFLP) markers. The Sec2 locus was localized between the Xiag57 and Xpsr109a loci in an 11 cM interval. The Sec5 locus co-segregated to Xiag57 and was tightly linked to the Sec2 locus at a map distance of 0.5cM.