<p><i>Colletotrichum sublineolum</i> is the causal agent of sorghum anthracnose, a very common and destructive fungal disease in warm and humid areas, especially in West and Central Africa. Use of host plant resistance is considered as the most important and effective control option for sorghum diseases. To achieve this goal, identification and mapping resistance genes is essential. In this study, we used an isolate of <i>C.</i> <i>sublineolum</i>, CsGL1, to screen our sorghum germplasm and identified a resistant inbred line, P9830. We developed a mapping population from a cross between P9830 and a susceptible line, TAM428, for this research. The population was advanced to the F₆ generation. Progenies were phenotyped at F₂, F₃ and F₆ generations for disease resistance against the pathogen, CsGL1. In the F₂ generation, 460 individuals showed resistance and 149 individuals showed susceptibility to CsGL1. This result fits the 3:1 segregation pattern expected for resistance controlled by a single gene. Bulked segregant analysis with next generation sequencing was used on selected F₆ recombinant inbred lines. A significant peak containing 153 SNPs was observed on the distal end of the long arm of chromosome 8. To verify resistance to CsGL1 was controlled by genes in this region, indel and SNP markers were used between 59.4Mbp and 60.6Mbp on chromosome 8 to fine map the resistance locus. One SNP marker located in the gene <i>Sobic.008G166400</i> co-segregated with resistance, and another two indel markers were discovered to be tightly linked to the resistance locus. These three PCR-based SNP markers would be useful for marker-assisted selection for improving anthracnose resistance against CsGL1. Two candidate genes, <i>Sobic.008G166400</i> and <i>Sobic.008G166550</i>, were found in the locus. Both of the genes encode LRR proteins implicated in plant disease defense response. The identity of DNA sequence between these two candidate genes is 94.1%, possibly the result of tandem duplication. Another possible ortholog in the region is <i>Sobic.008G167500</i>. Quantitative PCR analysis showed that the expression level of <i>Sobic.008G166400</i> didn’t change significantly in a resistant RIL, 17-12 but was induced in a susceptible RIL, 13-31, after CsGL1 infection. In conclusion, we mapped two candidate genes conferring resistant to CsGL1 on chromosome 8, and <i>Sobic.008G166400</i> is more likely of the two to be determined as the gene controlling resistance to CsGL1. </p>

<p>Identifikacija genomskih regiona na koje je delovala selekcija tokom stvaranja elitnih<br />sorti soje (<em>Glycine max</em> (L.) Merr.) može ukazati na pozicije gena koji determini&scaron;u<br />važna agronomska svojstva ili su odgovorni za adaptabilnost. U radu su sagledani<br />efekti oplemenjivanja u agroklimatskim uslovima centralne i istočne Evrope koristeći<br />pristup&nbsp; &ldquo;<em>hitchhiking</em>&rdquo;&nbsp; mapiranja i analizu&nbsp; pedigrea. U ovu svrhu&nbsp; su&nbsp; primenjeni<br />molekularni markeri, mikrosateliti i&nbsp; principi populacione genetike, koristeći vi&scaron;e<br />različitih pristupa za identifikaciju selektivno značajnih lokusa. Analiza je obuhvatila<br />populacije soje koje su se sastojale od predačkih genotipova i elitnih genotipova koji<br />su nastali u Institutu za ratarstvo i povrtarstvo u Novom Sadu. Analizom pedigrea je<br />potvrđena uska genetička osnova sorti soje elitne populacije.&nbsp; Kao posledica<br />dugogodi&scaron;njeg oplemenjivanja, svi analizirani parametri su&nbsp; ukazali na statistički<br />značajno smanjenje genetičkog diverziteta elitne populacije u odnosu na predačku.<br />Usled specifične strukture populacija soje, koja je u velikoj meri bila pod uticajem<br />pedigrea&nbsp; elitnih genotipova,&nbsp; uočen je nizak nivo genetičke diferencijacije među<br />ispitivanim populacijama. Primenom najmanje dva različita pristupa identifikovano je<br />devet mikrosatelitskih lokusa koji su ukazivali na regione genoma na koje je delovala<br />selekcija,&nbsp; a koji su bili uključeni u proces adaptacija u agroklimatskim uslovima<br />centralne i istočne Evrope.&nbsp; U elitnoj populaciji je potvrđeno povećanje stope<br />gametskog disekvilibrijuma, najverovatnije kao posledica delovanja selekcije.<br />&bdquo;<em>Bottleneck</em>&rdquo; test je ukazao na značajno smanjenje diverziteta samo kod lokusa na koje je&nbsp; delovala&nbsp; selekcija&nbsp; u&nbsp; elitnoj&nbsp; populaciji, &scaron;to&nbsp; najverovatnije&nbsp; nije uzrokovano<br />demografskim faktorima, nego takođe predstavlja posledicu delovanja selekcije.<br />Analizom kolokacije poznatih QTL regiona i identifikovanih, selektivno značajnih<br />genomskih regiona, uočeno je ukupno 264 QTL-ova, od kojih su najzastupljeniji bili<br />lokusi koji su determinisali svojstva u vezi sa reproduktivnim razvojem biljke.<em> In silico</em><br />analizom je utvrđeno&nbsp; da su lokusi&nbsp; na koje je delovala selekcija,&nbsp; determinisali<br />agronomski značajna svojstva&nbsp; koja su na direktan ili indirektan način&nbsp; uticala na<br />povećanje prinosa elitnih sorti soje u specifičnim agroklimatskim uslovima gajenja.<br />Rezultati istraživanja su takođe ukazali da E1 gen, koji ima važnu ulogu u regulisanju<br />vremena cvetanja i sazrevanja kod soje, ili region u okolini ovog gena, verovatno ima<br />glavni&nbsp; uticaj&nbsp; na&nbsp; adaptaciju&nbsp; na&nbsp; agroklimatske&nbsp; uslove&nbsp; područja&nbsp; centralne&nbsp; i&nbsp; istočne<br />Evrope. Takođe se pretpostavlja da je najveći broj selektivno značajnih gena imao<br />regulatornu ulogu, delujući kao&nbsp; transkripcioni faktori, kao i ulogu u&nbsp; procesima<br />transporta.&nbsp; Identifikovani&nbsp; selektivno&nbsp; značajni&nbsp; genomski&nbsp; regioni&nbsp; u&nbsp; okviru<br />oplemenjivačkog programa mogu imati praktičnu primenu u povećanju efikasnosti<br />oplemenjivanja u narednom periodu.</p> / <p>The identification of genomic regions affected by selection during breeding of soybean<br />(<em>Glycine max</em> (L.) Merr.) may indicate the positions of important agronomic traits<br />genes or genes underlying adaptation to a specific target environment. This study<br />investigated the effects of breeding in Central-East European environments by a<br /><em>hitchhiking </em>mapping approach and pedigree analysis. Population genetic principles<br />were applied to microsatellite markers using multiple outlier detection tests. The<br />analysed populations comprised ancestral genotypes and elite varieties, developed at<br />the Institute of Field and Vegetable Crops, Novi Sad. The pedigree analysis confirmed<br />narrow genetic base of elite genotypes. As a result of long-term breeding, all analysed<br />parameters showed significant reduction in genetic diversity in the elite population,<br />compared to the ancestral. Specific population structure of analysed varieties, which<br />has been largely influenced by the pedigree, probably caused a low level of genetic<br />differentiation between the populations. Using at least two approaches, nine markers<br />were considered as strong positive selection candidates, indicating regions involved in<br />the adaptation to Central-East Europe environments. Also, an excess of linkage<br />disequilibrium was confirmed in the elite population, probably caused by selection.<br /><em>Bottleneck</em> tests provided evidence of population bottlenecks only for the candidate<br />positive selection loci in the elite population, suggesting that selection might shaped<br />the pattern of genetic diversity in these regions. The co-localisation analysis of the<br />candidate positive selection loci and previously mapped quantitative trait loci (QTLs),<br />identified in total 264 QTLs in selectively important genomic regions. The highest<br />number of identified QTLs had impact on the reproductive period.<em> In silico </em>analysis<br />revealed a high level of agreement between the identified QTLs and the traits expected<br />to be under selection during soybean breeding, indicating that selection was mostly<br />directed towards increasing the yield of elite varieties in a specific environmental<br />conditions. Furthermore, E1 gene that controls flowering time and maturity in soybean,<br />or its surrounding region, seems to be a major contributor for adaptation to<br />environmental conditions of Central-East Europe. It is assumed that most of the<br />selectively important genes had regulatory role, acting as transcription factors, as well<br />as a role in the processes of transport. The identified selectively important genomic<br />regions in a specific breeding program could have practical importance for future<br />breeding and yield improvement.</p>

The influence of genetic variability on the response of the five rice varieties, Cica, Starbonett, Lemont, Bluebonett X IR 43, and IR43, to applied zince at 0, 10, 20 and 40 kg Zn ha^-1 under varying cellulose and water management conditions was studied in a greenhouse experiment. Typical zinc deficiency symptoms, varying in intensity among varieties, were nted, especially in the zero applied zinc treatments. Zinc deficiency symptoms were characterised by blanching at the base of the emerging leaves and rusty brown discolouration in the older leaves.

The influence of genetic variability on the response of the five rice varieties, Cica, Starbonett, Lemont, Bluebonett X IR 43, and IR43, to applied zince at 0, 10, 20 and 40 kg Zn ha^-1 under varying cellulose and water management conditions was studied in a greenhouse experiment. Typical zinc deficiency symptoms, varying in intensity among varieties, were nted, especially in the zero applied zinc treatments. Zinc deficiency symptoms were characterised by blanching at the base of the emerging leaves and rusty brown discolouration in the older leaves.

Thesis (Ph.D.) - University of KwaZulu-Natal, Pietermaritzburg, 2009. / Submitted to the African Centre for Crop Improvement. Full text also available online. Scroll down for electronic link.

Thesis (Ph.D.) - University of KwaZulu-Natal, Pietermaritzburg, 2007. / Full text also available online. Scroll down for electronic link.

Thesis (MScAgric.)--University of Stellenbosch, 2001. / ENGLISH ABSTRACT: In cross pollinated crops, recurrent selection is used to increase the frequency of desirable alleles by breaking up existing linkage blocks and forming new gene combinations. Despite promising results from numerous feasibility studies, recurrent selection is seldom routinely used in wheat. A major obstacle has been the inability to readily achieve random interbreeding of large numbers of selected plants. In China the Taigu genetic male sterility gene, Ms2, has however been used to establish a recurrent selection programme in which field grown male sterile plants were pollinated by selected male fertile plants (Huang et al., 1988). Another dominant gene for male sterility, Ms3, was found after EMS treatment of the seeds of an alloplasmie common wheat with Triticum tauschii cytoplasm (Maan et al., 1984) and is located at 3 map units from the centromere on chromosome arm SAS (Maan et al., 1987). In a study done during 1999 at Welgevallen to determine the frequency of natural intererossing under field conditions, Ms3 showed incomplete penetrance and only about two thirds of the seed set on male sterile plants could be attributed to intercrossing. Ms3 has stable expression in plants grown within the normal range of greenhouse temperatures for wheat, 16 - 2SoC. Under warmer field conditions, 21 - 3SoC, its penetrance is, however, incomplete (Maan et al., 1984). The utility of Ms3 under field conditions is therefore unsatisfactory. An attempt to determine the location and origin of an unknown male sterility gene, found in cross 9SK3 of a routine breeding programme, showed that a single locus was not the cause of the male sterility. Chromosome abnormalities and gene imbalances were probably to blame. The male sterility probably relates to a T.urartu addition chromosome in the pedigree of cross 9SK3. To facilitate the production of large numbers of hybrid progeny, a simple hydroponic system was developed in which male sterile tillers cut at the flowering stage can be pollinated and maintained for about 8 weeks, long enough to produce viable seeds. For pollination, florets on male tillers are cut open and placed in a container with a similar number of pollen shedding male tillers. It was found that cut tillers could be maintained in the hydroponic system as long as certain precautions were met: (a) The tillers must be handled with care so as not to damage the flag leaf which must be maintained for as long as period possible. (b) The tillers have a nutrient requirement and a 20% solution showed the best results of the nutrient solutions tested. (c) The sterilizing effect of Jik at O.OS%gave excellent fungal control en helped to sustain the nutrient solution. (d) Although the treatment of tillers with hormones improved seed quality, it was not justified by the additional inputs required. Different selection strategies were used for male and female plants. At the onset of the recurrent selection programme in 1998, a total of 1881 plants were tested for seedling resistance and 597 plants were selected for use as parents and source material for 1999. In total 158 male sterile and 188 male fertile ears were used in the hydroponic pollination and a 63.47% seed set was obtained, resulting in 3410 seeds, forming the 1999 female component. One hundred and fifty seven F2:96K109plants were selected from a field grown population in 1998. These, together with 44 selections from a pedigree programme, formed the male component for 1999. In total 9564 plants were tested for seedling resistance during 1999. A total of 3230 resistant seedling were selected and planted. Again male fertile plants from the previous season were field planted and selected. The selected plants were subjected to mixograph testing. A total of 448 male sterile and 1020 male fertile ears were used for hydroponic pollination. Approximately 12000 seeds were harvested, the seed set being around 75%. The 157 F2:96K109 field selected plants (1999) and 64 selections from a pedigree programme formed the male component for 2000. Seedling resistance testing during 2000 included a total of 6465 plants and 2832 were selected and planted. The hydroponic system was improved during 2000 with new, larger capacity containers being used which improved cross pollination. In total 878 male sterile tillers and 1016 male fertile tillers were cut and intercrossed. In total 25380 seeds were harvested, the seed set being 81.7%. In an attempt to determine the amount of variation within the 157 F2-families selected during 1999, mixograph testing was performed. The data showed variation among families. Seedling resistance testing for leaf and stem rust was performed on the 1999 and 2000 FIs to determine the variation for resistance within the populations. Both populations showed high level of stem rust resistance but lower levels of leaf rust resistance (± 50%). Ms3 can thus be used in combination with hydroponic tiller culture to facilitate recurrent selection. Integration with an excisting pedigree selection programme is viable and requires little additional input. Some of the these results have already been published (Addendum D). / AFRIKAANSE OPSOMMING: Herhalende seleksie word by kruisbestuiwers aangewend om die frekwensie voordelige allele te verhoog deur die opbreek van bestaande koppelingsblokke en vorming van nuwe geen-kombinasies. Hoewel uitstekende resultate m.b.V.herhalende seleksie reeds by koring verkry is, is die roetine aanwending egter beperk weens die gebrek aan effektiewe kruisbestuiwing van groot getalle plante. In China is "Taigu" genetiese manlike steriliteit, Ms2, egter met sukses aangewend vir die vestiging van 'n herhalende seleksieprogram vir landverboude koring. Die manlik-vrugbare plante word vir die bestuiwing van geselekteerde manlik-steriele plante aangewend (Huang et al., 1988). Nog 'n dominante manlike steriliteitsgeen, Ms3, is ontdek na EMS behandeling van sade afkomstig vanaf 'n alloplasmiese gewone koring met 'n Triticum tauschii sitoplasma (Maan et al., 1984) en is gesetelop chromosoom 5AS, 3 kaarteenhede vanaf die sentromeer (Maan et al., 1987). 'n Ondersoek na die frekwensie natuurlike kruisbestuiwing onder landtoestande (Welgevallen, 1999) het getoon dat onvolledige penetrasie van Ms3 lei tot ongeveer 5% selfbestuiwing en dat slegs twee-derdes van die saadset aan kruisbestuiwing toegeskryf kon word. Ms3 word wel stabiel uitgedruk onder normale glashuistemperature tydens blom nl. 16 - 25°C, maar onder warmer landtoestande, 21 - 35°C, is uitdrukking onstabiel met laer penetrasie van die geen (Maan et al., 1984). Die benutbaarheid van Ms3 onder landtoestande was dus onbevredigend. Die ondersoek na die oorsprong en ligging van 'n onbekende, manlike steriliteitsgeen (95K3) wat ontdek is in 'n roetine teelprogram het daarop gedui dat 'n enkellokus waarskynlik me ter sprake is nie, maar eerder chromosoom-abnormaliteite en geenwanbalanse. Die manlike steriliteit kan verband hou met 'n T urartu addisie chromosoom in die stamboom van hierdie bron. Ten einde kruisbestuiwing van 'n groot aantal plante te bewerkstellig, is 'n eenvoudige bestuiwersisteem ontwikkel gegrond op waterkultuurkweking van afgeknipte manlik-steriele (Ms3ms3), are. Manlik-steriele en manlik-vrugbare are is tydens blom geknip. Die manliksteriele are se blommetjies is oopgeknip en toegelaat om deur die manlik-vrugbare are bestuif te word. Die bestuifde manlik-steriele are (Ms3ms3) is hierna vir ongeveer 8 weke gelaat vir saadvorming. Afgeknipte are kan baie suksesvol in voedingsmedium onderhou word mits sekere eenvoudige voorsorgmaatreëls getref word, naamlik: (a) Die are moet met sorg hanteer word en die vlagblaar moet so lank as moontlik behou word. Are moet weekliks teruggeknip word ten einde verstopping en agteruitgang van vaatweefsel teen te werk. Die oorspronklik- afgeknipte halm is dus belangrik. (b) Die are toon 'n definitiewe voedingsbehoefte en 'n 20% voedingsoplossing was die beste van die oplossings wat getoets is. Die voedingsoplossing moet verkieslik weekliks vervang word wanneer are teruggeknip word. Op die tydstip behoort die houers met 'n steriliseringsmiddel gewas te word vir die verwydering van enige moontlike swamgroei aan die houers se wande. (c) Jik was die beter steriliseringsmiddel en het teen 0.05% toediening goeie swaminhibering bewerkstellig. (d) Hormone is nie in die roetinetoepassing gebruik nie aangesien die voordeel hiervan nie die ekstra insette regverdig nie. Verskillende strategieë is aangewend vir die seleksie van manlike en vroulike plante. Met die aanvang van die herhalende seleksieprogram in 1998 is 'n totaal van 1881 plante getoets vir roesweerstand en 597 geselekteer as bronmateriaal vir 1999. In totaal is 158 manliksteriele en 188 manlik-vrugbare are gebruik in die bestuiwersisteem vir die verkryging van die 1999 vroulike komponent. 'n Totaal van 3410 sade is verkry met 'n 63.47% saadset. Tesame met 157 F2:96KI09 landgeselekteerde plante is 44 seleksies vanuit 'n stamboom seleksieprogram gebruik as manlike komponent in 1999. Gedurende 1999 is 9564 plante getoets vir roesweerstand en 3230 geselekteer en geplant. Weereens het landseleksie plaasgevind. Die 157 seleksies is onderwerp aan miksograaf-toetsing. Vierhonderd agt- en - veertig manlik-steriele en 1020 manlik-vrugbare are is gebruik in die bestuiwersisteem. Ongeveer 12138 sade is geoes, teen 'n 75% saadset. Gedurende 2000 is die sade asook 64 seleksies uit 'n stamboom seleksieprogram aangewend as die manlike komponent. Roestoetsing is weereens in 2000 uitgevoer en 6465 plante is geïnokuleer waaruit 2832 plante geselekteer en geplant is. Die bestuiwersisteem is aangepas vir die hantering van groter aantalle are tydens 2000 en in totaal is 878 manlik-steriele are en 'n 1016 manlik-vrugbare are gebruik vir kruisbestuiwing. Die saadset is verhoog na 81.7% en 25380 sade is verkry. Om die hoeveelheid variasie binne die populasie te bepaal, is miksograaftoetsing op die 1999 F2-populasie uitgevoer. Die data het aangetoon dat groot hoeveelhede genetiese variasie beskikbaar is binne die populasie. Roestoetsing van die 1999- en 2000-bestuiwerpopulasies is ook uitgevoer om 'n indikasie te verkry van die verspreiding van weerstand teen blaar- en starnroes. Die blaamoes het 'n relatief lae vlak van weerstand getoon (± 50%) terwyl die stamroesweerstand baie hoë vlakke gehandhaaf het. Ms3 kan dus gebruik word om in kombinasie met waterkultuurkweking van gesnyde halms, 'n herhalende seleksieprogram van stapel te stuur. Integrasie met 'n bestaande stamboom seleksieprogram is ook moontlik en sal relatief min addisionele insette vereis. 'n Gedeelte van die werk is reeds gepubliseer en word hierbyaangeheg as Aanhangsel D.

<p>Plant microbiomes are increasingly recognized for their potential to help plants with critical functions such as nutrient acquisition. Nitrogen is the most limiting nutrient in agriculture and growers apply substantial amounts to meet crop needs. Only 50% of N fertilizers are generally taken up by plants and the rest is subject to loss which negatively affects environmental quality. Organic fertilizers such as cover crops and animal manure can help reduce this loss, though these materials must mineralize via microbial mediated processes before they are available for plant uptake, which makes managing fertility using these sources difficult. Some plants can scavenge nutrients from organic materials by stimulating positive priming processes in soil. Carrot (<i>Daucus carota.</i> L) is known as an N scavenging crop, making it an ideal model crop to study these interactions. In a greenhouse trial, soils were amended with an isotopically labeled corn residue to track N movement, and planted with one of five carrot genotypes expected to differ in nitrogen use efficiency (NUE). Changes in soil b-glucosidase activity, ammonium (NH₄⁺-N) and nitrate (NO₃^--N) concentrations, soil bacterial community composition, weight and carbon and N concentrations, and total δ¹⁵N of above and below ground carrot biomass were determined. Results indicate that there are genetic differences in the ability of carrots to promote priming under N limited conditions, which could be exploited to enhance NUE in carrots. Soil microbial communities differed between genotypes, indicating that some of these microbes could play a role in the differential N scavenging responses observed, and/or contribute to other important functions such as resistance to pests. Endophytic microbes residing inside carrot taproots also have potential to contribute to NUE and other benefits, but are notoriously difficult to isolate and culture. New next generation sequencing technologies have revolutionized the study of microbiomes, though using these tools to study bacterial endophytes in plants is still difficult due to co-amplification of plant organelles. Consequently, a second study was conducted to determine if subjecting carrot tissues to hollow fiber microfiltration followed by enzymatic digestion could enhance recovery and amplification of bacterial endophytes. Carrot taproot digests were subject to amplification using a standard V3-V4 16S primer set, as well as two alternative (blocking and mismatch) primer sets that have prevented amplification of plastids/mitochondria in other plant species. Results indicate that the microfiltration/digestion procedure can increase the number of bacterial endophyte OTUs assigned and could be further optimized for use in carrots. The blocking and mismatch primer sets were not as effective in blocking co-amplification of plant products as they are in other studies, possibly due to the presence of a high number of chromoplasts in carrot tissues. Taxonomic assignment of bacterial endophytes differed significantly between the primer sets, indicating that multiple primer sets may be needed to fully characterize these communities in carrots. The enzymatic digestion procedure could artificially inflate certain taxa, which could be helpful if targeting specific taxa. These studies demonstrate that carrots are intimately connected with microbes residing in the soil and within their taproots, and further exploration of these plant-soil-microbial relationships could enhance the yield and sustainability of carrot production systems.</p>

<p>Phytophthora root and stem rot (PRSR), caused by oomycete <i>Phytophthora sojae</i>, is the most severe soil-borne disease of soybean (<i>Glycine max</i> (L.) Merr.) worldwide. The disease can be effectively managed by introducing resistance to <i>P. sojae</i> (<i>Rps</i>) genes into soybean cultivars by breeding, which requires continuous efforts on identification of resistance resources from soybean germplasm. Previously, two resistance genes, <i>Rps2-cas</i> (former name <i>Rps2-das</i>) and <i>Rps14 </i>(former name<i> Rps1-f</i>), were mapped by linkage analysis from soybean landraces, PI 594549 C and PI 340029, respectively. The resistance underlying PI 594592 also need further characterization given its broad resistance spectrum. In this study, <i>Rps-2cas</i> and <i>Rps14</i> were further mapped, and <i>Rps2-b</i>, was identified and initial mapped from PI 594592. Thus, this thesis research was divided into three parts for three <i>Rps</i> genes.</p><p>The first part mainly focuses advances on <i>Rps2-cas</i>. Marker-assisted spectrum analysis was performed for <i>Rps-2cas</i> to confirm its potential in disease management. A high-quality genome assembly of PI 594549 C was generated, and KASP markers were developed based on comparison between new reference and Williams 82 reference genome. The gene was further mapped to a 32.67-kb region on PI 594549 C reference genome harboring three expressed NLRs by 24 recombinants screened from a large F₄ population. Comparative genomics analysis suggests the only intact NBS-LRR gene in the fine mapping region is the best candidate gene for <i>Rps2cas</i>, and its function was validated by stable transformation. Evidences from other high-quality assembly genomes suggest <i>Rps2-cas</i> originated from an ancient unequal crossing over event.</p> <p>In the second part, <i>Rps14</i> was further mapped using 21 recombinants identified from a F₃population consisting of 473 plants. In commonly used Williams 82 reference genome, the assembly of fine mapping region was incomplete, and <i>Rps14</i> region showed drastic variation in size and copy number of NLRs in 23 high-quality genome assemblies, suggesting the complexity of <i>Rps14</i> region and high-quality reference sequence of donor line is required for isolation of <i>Rps14</i> candidate genes. Marker assisted resistance test showed <i>Rps14</i> had wider resistance spectrum to different <i>P. sojae </i>isolates comparing to other <i>Rps</i> genes on chromosome 3, and phylogenic analysis further supported the potential of <i>Rps14</i> to be a novel resistance gene. </p> <p>For the third part, an F₂population derived from a cross between PI 594592 and Williams was tested by <i>P. sojae</i> race 1. The 3:1 and 1:2:1 Mendelian segregation ratios were observed in F₂individuals and F_2:3families, respectively, suggesting a single dominant <i>Rps</i> gene in PI 594592. The gene was initially mapped to the distal end chromosome 16 overlapped with <i>Rps2</i>, and the gene was tentatively named as <i>Rps2-b</i>. Polymorphic SSR markers and InDel markers designed based on re-sequencing data of PI 594592 and Williams was used to genotyping all the F_2:3families, and a linkage map was constructed for <i>Rps2-b</i>. <i>Rps2-b</i> was mapped to a 461.8-kb region flanked by SSR marker Satt431 and InDel marker InDel3668 according to the reference genome (Wm82. a2). Marker-assisted resistance test showed <i>Rps2-b</i> hold a wide resistance spectrum. </p>

<p> Fruit size is a polygenic trait controlled by multiple genomic regions each with small effect. The complex nature of fruit size regulation makes it challenging to dissect individual genes responsible for phenotypic variation. Though recent advances in high-throughput genome sequencing technology in conjunction with improved statistical and computational methods empowered science to explicitly understand the genetic basis underlying multiple fruit quality traits, much of the work that has been done through classical quantitative trait loci (QTL) approach resulted in reduced resolution and instability when evaluating in different genetic backgrounds and different environments. To increase the precision and improve the stability of QTL analyses and to identify genes controlling fruit size, we performed a set of multiple quantitative and molecular genetic analyses to elucidate the underlying genetic architecture of fruit mass. A total of nine genomic regions associated with fruit mass were identified, two of which are novel to this study; markers Md14_26050918 and Md14_26050904. Detected QTLs explained ~ 42% of the total genetic variation of which ~ 20% is explained by the two novel QTLs. Regions responsible for fruit mass variation appear to be under strong additive and epistatic genetic control. These regions exhibited high stability across-family as well as across-years and showed accurate genomic prediction across-family. Additionally, we identified the apple gene family of putative fw2.2 orthologs, naming them Cell Number Regulators (CNRs) genes (MdCNRs). Three CNRs (MdCNR1-3) showed increased expression at early fruit growth in small-fruited crabapple, associating with reduced relative cell production rate (RCPR), suggesting that alteration in cell number that leads to a subsequent reduction in fruit size is probably due to reduced cell division most likely due to changes in CNRs regulation. Furthermore, our study revealed that reduced fruit size is partially due to the shortened cell expansion period after which cell expansion ceases in the small-fruited crabapple species. Together, these data will advance our understanding of dissecting fruit mass genetic architecture and have high potential to be deployed for marker-assisted selection and further breeding approaches. </p>