Founder Parents Research Articles

Registration of sorghum backcross‐nested association mapping (BC‐NAM) families in a BTx623 or RTx436 background

AbstractTwo sorghum [Sorghum bicolor (L.) Moench] backcross‐nested association mapping (BC‐NAM) populations (Reg. no. MP‐5, NSL 546724 MAP) have been developed, composed of 30 families totaling 2189 BC1F4 lines using an elite maintainer (B) or restorer (R) line as the recurrent parent. The families were derived from unadapted founder lines that were backcrossed to BTx623 and/or RTx436 based on the fertility reaction score and phylogenetic analysis of the founder lines. These unadapted founder lines were selected based on agronomic fitness, breeder desirability, and genetic diversity and represent a range of races and working groups. The 30 families were developed from 27 founder parents—three of the founder parents were backcrossed to both recurrent parents to provide a genetic relationship across all 30 families. Each family consists of 45–100 BC1F4 lines selected for standard agronomic fitness, and each population was genotyped using genotype‐by‐sequencing. To identify families that possess (or segregate for) traits of interest, 13 lines from each population were randomly selected and phenotyped for a range of agronomic and stress tolerance traits. These BC‐NAM populations, which are adapted to US production regions and possess novel genetic diversity, have application in genetic research as a mapping resource for traits of interest and for sorghum breeding programs to diversify R and B line parental heterotic pools.

Integrated IBD Analysis, GWAS Analysis and Transcriptome Analysis to Identify the Candidate Genes for White Spot Disease in Maize.

Foundation parents (FPs) play an irreplaceable role in maize breeding practices. Maize white spot (MWS) is an important disease in Southwest China that always seriously reduces production. However, knowledge about the genetic mechanism of MWS resistance is limited. In this paper, a panel of 143 elite lines were collected and genotyped by using the MaizeSNP50 chip with approximately 60,000 single nucleotide polymorphisms (SNPs) and evaluated for resistance to MWS among 3 environments, and a genome-wide association study (GWAS) and transcriptome analysis were integrated to reveal the function of the identity-by-descent (IBD) segments for MWS. The results showed that (1) 225 IBD segments were identified only in the FP QB512, 192 were found only in the FP QR273 and 197 were found only in the FP HCL645. (2) The GWAS results showed that 15 common quantitative trait nucleotides (QTNs) were associated with MWS. Interestingly, SYN10137 and PZA00131.14 were in the IBD segments of QB512, and the SYN10137-PZA00131.14 region existed in more than 58% of QR273's descendants. (3) By integrating the GWAS and transcriptome analysis, Zm00001d031875 was found to located in the region of SYN10137-PZA00131.14. These results provide some new insights for the detection of MWS's genetic variation mechanisms.

Precisely mapping a major QTL for grain weight on chromosome 5B of the founder parent Chuanmai42 in the wheat-growing region of southwestern China.

QTgw.saas-5B was validated as a major thousand-grain weight-related QTL in a founder parent used for wheat breeding and then precisely mapped to a 0.6 cM interval. Increasing the thousand-grain weight (TGW) is considered to be one of the most important ways to improve yield, which is a core objective among wheat breeders. Chuanmai42, which is a wheat cultivar with high TGW and a high and stable yield, is a parent of more than 30 new varieties grown in southwestern China. In this study, a Chuanmai42-derived recombinant inbred line (RIL) population was used to dissect the genetic basis of TGW. A major QTL (QTgw.saas-5B) mapped to the Xgwm213-Xgwm540 interval on chromosome 5B of Chuanmai42 explained up to 20% of the phenotypic variation. Using 71 recombinants with a recombination in the QTgw.saas-5B interval identified from a secondary RIL population comprising 1818 lines constructed by crossing the QTgw.saas-5B near-isogenic line with the recurrent parent Chuannong16, QTgw.saas-5B was delimited to a 0.6cM interval, corresponding to a 21.83Mb physical interval in the Chinese Spring genome. These findings provide the foundation for QTgw.saas-5B cloning and its use in molecular marker-assisted breeding.

Cytological and genetic effects of rye chromosomes 1RS and 3R on the wheat-breeding founder parent Chuanmai 42 from southwestern China.

The online version contains supplementary material available at 10.1007/s11032-023-01386-0.

Conservatively transmitted alleles of key agronomic genes provide insights into the genetic basis of founder parents in bread wheat (Triticum aestivum L.)

BackgroundFounder parents play extremely important roles in wheat breeding. Studies into the genetic basis of founder parents and the transmission rules of favorable alleles are of great significance in improving agronomically important traits in wheat.ResultsHere, a total of 366 founder parents, widely grown cultivars, and derivatives of four representative founder parents were genotyped based on efficient kompetitive allele-specific PCR (KASP) markers in 87 agronomically important genes controlling yield, quality, adaptability, and stress resistance. Genetic composition analysis of founder parents and widely grown cultivars showed a consistently high frequency of favorable alleles for yield-related genes. This analysis further showed that other alleles favorable for resistance, strong gluten, dwarf size, and early heading date were also subject to selective pressure over time. By comparing the transmission of alleles from four representative founder parents to their derivatives during different breeding periods, it was found that the genetic composition of the representative founder parents was optimized as breeding progressed over time, with the number and types of favorable alleles carried gradually increasing and becoming enriched. There are still a large number of favorable alleles in wheat founder parents that have not been fully utilized in breeding selection. Eighty-seven agronomically important genes were used to construct an enrichment map that shows favorable alleles of four founder parents, providing an important theoretical foundation for future identification of candidate wheat founder parents.ConclusionsThese results reveal the genetic basis of founder parents and allele transmission for 87 agronomically important genes and shed light on breeding strategies for the next generation of elite founder parents in wheat.

Genetic characterization and comparative assessment of response of biparental and multi-parental populations to northern corn leaf blight in maize (Zea mays L.)

To compare the efficiency of multiparental and biparental progenies to northern corn leaf blight (NCLB) resistance, F3 progenies were evaluated during two seasons. A total of 418 F3 progenies derived from multiple founder parents and 248 F3 progenies derived from two parents, namely, SKV50 (Resistant) and CM202 (Susceptible) were phenotyped for their response to the NCLB during summer and kharif 2020. A wide range of disease severity was observed among F3 progenies derived from multiple parents ranging from 28.12 to 62.93%. The difference in the variances between multiparent and biparental progenies was indicated by the significance of Levene’s test. High genotypic and phenotypic coefficient of variation was observed among multi-parental progenies than those derived from the biparental population. Reaction to NCLB showed moderate heritability of 57% and high genetic advance as per cent mean (20.70%) in the case of biparental population, whereas, multi-parental population exhibited a high heritability (68%) and high genetic advance as per cent mean (28.57%). The distribution of F3 progenies was found to be positively skewed and platykurtic indicating that the trait was under the control of large number of genes with complementary gene action.

Genotype-by-culture-system interaction in catla and silver carp: Monoculture and biculture

Catla (Catla catla) and silver carp (Hypophthalmichthys molitrix) are globally significant aquaculture species, primarily grown in polyculture. The objectives of the current study were to i) quantify genetic differences among founder populations (i.e. genetic groups) of family-based genetic improvement programs ii) estimate genetic parameters for harvest weight under different culture systems (i.e. monoculture and biculture) and iii) determine the extent of genotype-by-culture-system interaction – a component of genotype-by-environment-by-management interaction. Founder parents were spawned to generate 188 catla and 184 silver carp base-population full-sibling families. Families were grown out in eight earthen ponds – two monoculture catla, two monoculture silver carp and four biculture – and harvest body weight and survival analysed. Neither interaction (i.e. heterosis) nor main effects among genetic groups were statistically significant in any pond, trait or species. Additive genetic variances were significantly different from zero in all but one pond in each species. Narrow-sense heritability estimates for harvest weight ranged from 0.06 to 0.44 for catla and from 0.18 to 0.51 for silver carp. In contrast to catla, silver carp inter-pond genetic correlations were significantly different from one in multiple cases, indicating the presence of genotype-by-pond interactions. However, these interactions were not entirely explained by genotype-by-culture-system interaction, given the genetic correlation between the monoculture ponds was 0.56 (P = 0.038; from one). Additive variances were not statistically significant for survival in either species, with the exception of silver carp in one polyculture pond. Notably catla harvest weight in monoculture ponds was substantially greater than in biculture ponds, indicating the presence of inter-species competition in biculture ponds.

Dissection of two QTL clusters underlying yield-related heterosis in the cabbage founder parent 01–20

Cabbage has significant heterosis and most commercial cultivars are hybrids. To explore genetic basis of cabbage heterosis and promote cabbage heterosis utilization, we constructed two populations by crossing 100 DH lines derived from a cabbage hybrid 01–20 × 96–100 with two female parents. Hybrids exhibited different extents of heterosis, the mean value of economic yield was 2.6 times bigger than parents. We identified 66 and 73 QTLs associated with mid-parent heterosis and transgressive heterosis of twelve yield-related traits, respectively. Some QTLs could be detected under the two-year experiment existed in two populations with different testers, showing relatively high phenotypic contribution rate (15.8%–20.0%). Heterosis QTLs exhibited clustered distribution in several cabbage chromosome regions. Two dominant genetic regions, mk300–316 and mk258–268, originated from the elite parent 01–20, exhibited significant genetic effects for yield-related heterosis, which were first identified. Three elite DH lines (D22, D46, D83) harboring these two dominant regions were selected as having strong heterosis in cabbage production. Candidate gene analysis revealed that some genes participating in biosynthetic processes of carbohydrates and some responses to auxin might affect cabbage yield heterosis. QTL identification and genetic dissection of yield-related traits provide new insights into the genetic effects of cabbage heterosis.

Identification and validation of QTLs for kernel number per spike and spike length in two founder genotypes of wheat

BackgroundKernel number per spike (KNS) and spike length (SL) are important spike-related traits in wheat variety improvement. Discovering genetic loci controlling these traits is necessary to elucidate the genetic basis of wheat yield traits and is very important for marker-assisted selection breeding.ResultsIn the present study, we used a recombinant inbred line population with 248 lines derived from the two founder genotypes of wheat, Bima4 and BainongAK58, to construct a high-density genetic map using wheat 55 K genotyping assay. The final genetic linkage map consists of 2356 bin markers (14,812 SNPs) representing all 21 wheat chromosomes, and the entire map spanned 4141.24 cM. A total of 7 and 18 QTLs were identified for KNS and SL, respectively, and they were distributed on 11 chromosomes. The allele effects of the flanking markers for 12 stable QTLs, including four QTLs for KNS and eight QTLs for SL, were estimated based on phenotyping data collected from 15 environments in a diverse wheat panel including 384 elite cultivars and breeding lines. The positive alleles at seven loci, namely, QKns.his-7D2–1, QKns.his-7D2–2, QSl.his-4A-1, QSl.his-5D1, QSl.his-4D2–2, QSl.his-5B and QSl.his-5A-2, significantly increased KNS or SL in the diverse panel, suggesting they are more universal in their effects and are valuable for gene pyramiding in breeding programs. The transmission of Bima4 allele indicated that the favorite alleles at five loci (QKns.his-7D2–1, QSl.his-5A-2, QSl.his-2D1–1, QSl.his-3A-2 and QSl.his-3B) showed a relatively high frequency or an upward trend following the continuity of generations, suggesting that they underwent rigorous selection during breeding. At two loci (QKns.his-7D2–1 and QSl.his-5A-2) that the positive effects of the Bima4 alleles have been validated in the diverse panel, two and one kompetitive allele-specific PCR (KASP) markers were further developed, respectively, and they are valuable for marker-assisted selection breeding.ConclusionImportant chromosome regions controlling KNS and SL were identified in the founder parents. Our results are useful for knowing the molecular mechanisms of founder parents and future molecular breeding in wheat.

Analysis of Genetic Regions Related to Field Grain Number per Spike From Chinese Wheat Founder Parent Linfen 5064.

Wheat founder parents have been important in the development of new wheat cultivars. Understanding the effects of specific genome regions on yield-related traits in founder variety derivatives can enable more efficient use of these genetic resources through molecular breeding. In this study, the genetic regions related to field grain number per spike (GNS) from the founder parent Linfen 5064 were analyzed using a doubled haploid (DH) population developed from a cross between Linfen 5064 and Nongda 3338. Quantitative trait loci (QTL) for five spike-related traits over nine experimental locations/years were identified, namely, total spikelet number per spike (TSS), base sterile spikelet number per spike (BSSS), top sterile spikelet number per spike (TSSS), fertile spikelet number per spike (FSS), and GNS. A total of 13 stable QTL explaining 3.91–19.51% of the phenotypic variation were found. The effect of six of these QTL, Qtss.saw-2B.1, Qtss.saw-2B.2, Qtss.saw-3B, Qfss.saw-2B.2, Qbsss.saw-5A.1, and Qgns.saw-1A, were verified by another DH population (Linfen 5064/Jinmai 47), which showed extreme significance (P < 0.05) in more than three environments. No homologs of reported grain number-related from grass species were found in the physical regions of Qtss.saw-2B.1 and Qtss.saw-3B, that indicating both of them are novel QTL, or possess novel-related genes. The positive alleles of Qtss.saw-2B.2 from Linfen 5064 have the larger effect on TSS (3.30%, 0.62) and have 66.89% in Chinese cultivars under long-term artificial selection. This study revealed three key regions for GNS in Linfen 5064 and provides insights into molecular marker-assisted breeding.

Genetic characterization of multi-parental population to sorghum downy mildew in maize

Sorghum downy mildew (SDM) is considered as one of the important diseases of maize in tropical and sub-tropical regions of the world. Though effective chemical measures are available for SDM management, developing resistant hybrids and their cultivation is a widely accepted option. The present study was aimed at the utility of multi-parental population in generating the variability for SDM resistance. A total of 288 F3 progenies derived from eight founder parents were phenotyped for SDM during summer and rainy season of 2020. High genotypic and phenotypic coefficient of variation was observed among the F3 progenies. Narrow sense heritability and genetic advance as per cent mean (GAM) for SDM resistance was found to be high, Among the 288 F3 progenies four progenies were found to be resistant and 17 were moderately resistant to SDM. The distribution of F3 progenies was platykurtic and positively skewed during summer season and negatively skewed during rainy season indicating that the trait was under the control of large number of genes with complimentary and duplicate gene action, respectively.

Genomic Selection and Genome-Wide Association Studies for Grain Protein Content Stability in a Nested Association Mapping Population of Wheat

Grain protein content (GPC) is controlled by complex genetic systems and their interactions and is an important quality determinant for hard spring wheat as it has a positive effect on bread and pasta quality. GPC is variable among genotypes and strongly influenced by the environment. Thus, understanding the genetic control of wheat GPC and identifying genotypes with improved stability is an important breeding goal. The objectives of this research were to identify genetic backgrounds with less variation for GPC across environments and identify quantitative trait loci (QTLs) controlling the stability of GPC. A spring wheat nested association mapping (NAM) population of 650 recombinant inbred lines (RIL) derived from 26 diverse founder parents crossed to one common parent, ‘Berkut’, was phenotyped over three years of field trials (2014–2016). Genomic selection models were developed and compared based on predictions of GPC and GPC stability. After observing variable genetic control of GPC within the NAM population, seven RIL families displaying reduced marker-by-environment interaction were selected based on a stability index derived from a Finlay–Wilkinson regression. A genome-wide association study identified eighteen significant QTLs for GPC stability with a Bonferroni-adjusted p-value &lt; 0.05 using four different models and out of these eighteen QTLs eight were identified by two or more GWAS models simultaneously. This study also demonstrated that genome-wide prediction of GPC with ridge regression best linear unbiased estimates reached up to r = 0.69. Genomic selection can be used to apply selection pressure for GPC and improve genetic gain for GPC.

Variation in Root System Architecture among the Founder Parents of Two 8-way MAGIC Wheat Populations for Selection in Breeding

Root system architecture (RSA) is a target for breeding crops with effective nutrient and water use. Breeding can use populations designed to map quantitative trait loci (QTL). Here we non-invasively phenotype roots and leaves of the 16 foundation parents of two multi-parent advanced generation inter-cross (MAGIC) populations, covering diversity in spring (CSIRO MAGIC) and winter (NIAB MAGIC) wheats. RSA components varied after 16 days in the upgraded, paper-based imaging platform, GrowScreen-PaGe: lateral root length 2.2 fold; total root length, 1.9 fold; and seminal root angle 1.2 fold. RSA components total and lateral root length had the highest root heritabilities (H2) (H2 = 0.4 for CSIRO and NIAB parents) and good repeatability (r = 0.7) in the GrowScreen-PaGe. These can be combined with leaf length (H2 = 0.8 CSIRO; 0.7 NIAB) and number (H2 = 0.6 CSIRO; 0.7 NIAB) to identify root and shoot QTL to breed for wheats with vigorous RSA and shoot growth at establishment, a critical phase for crop productivity. Time resolved phenotyping of MAGIC wheats also revealed parents to cross in future for growth rate traits (fastest: Robigus–NIAB and AC Barrie–CSIRO; slowest Rialto–NIAB and G204 Xiaoyan54–CSIRO) and root: shoot allocation traits (fast growers grew roots, notably laterals, quicker than leaves, compared to slow growers).

Variability and Trait Association Studies for Late Leaf Spot Resistance in a Groundnut MAGIC Population

Globally, late leaf spot (LLS), a foliar fungal disease is one of the most important biotic constraint in groundnut production. Multi-Parent Advanced Generation Inter Cross (MAGIC) groundnut population was developed in a convergent crossing scheme using eight founder parents to develop a mapping population for multiple traits includes LLS. The experiments conducted in light chamber using detached leaf assay, and disease field screening nurseries at two locations (ICRISAT and ARS, Kasbe Digraj) showed significant variability for LLS resistance and component of resistance traits. Total 10 MAGIC lines with longer incubation (&gt;11.0 days) and two MAGIC lines with longer latent period (&gt;27 days) than the resistant parent, GPBD 4 were identified. The MAGIC lines, ICGR 171413, and ICGR 171443 with a lesion diameter of &lt;1 mm and 4.10–5.67% of leaf area damage can be valuable sources for the alleles limiting the pathogen severity. A total of 20 MAGIC lines recorded significantly superior for disease score at 105 DAP_I (5.60–6.89) compared to resistant check, GPDB 4 (6.89). Further studies to determine the type and number of genes controlling the LLS component traits in groundnut will be useful for improvement of resistance to LLS. Genomic selection approach can be valuable in groundnut breeding to harness the minor alleles contributing to the component traits of LLS resistance.

Enhanced stripe rust resistance obtained by combining Yr30 with a widely dispersed, consistent QTL on chromosome arm 4BL.

YrFDC12 and PbcFDC, co-segregated in chromosome 4BL, and significantly interacted with Yr30/Pbc1 to enhance stripe rust resistance and to promote pseudo-black chaff development. Cultivars with durable resistance are the most popular means to control wheat stripe rust. Durable resistance can be achieved by stacking multiple adult plant resistance (APR) genes that individually have relatively small effect. Chinese wheat cultivars Ruihua 520 (RH520) and Fengdecun 12 (FDC12) confer partial APR to stripe rust across environments. One hundred and seventy recombinant inbred lines from the cross RH520 × FDC12 were used to determine the genetic basis of resistance and identify genomic regions associated with stripe rust resistance. Genotyping was carried out using 55K SNP array, and eight quantitative trait loci (QTL) were detected on chromosome arms 2AL, 2DS, 3BS, 4BL, 5BL (2), and 7BL (2) by inclusive composite interval mapping. Only QYr.nwafu-3BS from RH520 and QYr.nwafu-4BL.2 (named YrFDC12 for convenience) from FDC12 were consistent across the four testing environments. QYr.nwafu-3BS is likely the pleiotropic resistance gene Sr2/Yr30. YrFDC12 was mapped in a 2.1-cM interval corresponding to 12Mb and flanked by SNP markers AX-111121224 and AX-89518393. Lines harboring both Yr30 and YrFDC12 displayed higher resistance than the parents and expressed pseudo-black chaff (PBC) controlled by loci Pbc1 and PbcFDC12, which co-segregated with Yr30 and YrFDC12, respectively. Both marker-based and pedigree-based kinship analyses revealed that YrFDC12 was inherited from founder parent Zhou 8425B. Fifty-four other wheat cultivars shared the YrFDC12 haplotype. These results suggest an effective pyramiding strategy to acquire highly effective, durable stripe rust resistance in breeding.

Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction.

Multi-parent Advanced Generation Inter-crosses (MAGIC) lines have mosaic genomes that are generated shuffling the genetic material of the founder parents following pre-defined crossing schemes. In cereal crops, these experimental populations have been extensively used to investigate the genetic bases of several traits and dissect the genetic bases of epistasis. In plants, genomic prediction models are usually fitted using either diverse panels of mostly unrelated accessions or individuals of biparental families and several empirical analyses have been conducted to evaluate the predictive ability of models fitted to these populations using different traits. In this paper, we constructed, genotyped and evaluated a barley MAGIC population of 352 individuals developed with a diverse set of eight founder parents showing contrasting phenotypes for grain yield. We combined phenotypic and genotypic information of this MAGIC population to fit several genomic prediction models which were cross-validated to conduct empirical analyses aimed at examining the predictive ability of these models varying the sizes of training populations. Moreover, several methods to optimize the composition of the training population were also applied to this MAGIC population and cross-validated to estimate the resulting predictive ability. Finally, extensive phenotypic data generated in field trials organized across an ample range of water regimes and climatic conditions in the Mediterranean were used to fit and cross-validate multi-environment genomic prediction models including G×E interaction, using both genomic best linear unbiased prediction and reproducing kernel Hilbert space along with a non-linear Gaussian Kernel. Overall, our empirical analyses showed that genomic prediction models trained with a limited number of MAGIC lines can be used to predict grain yield with values of predictive ability that vary from 0.25 to 0.60 and that beyond QTL mapping and analysis of epistatic effects, MAGIC population might be used to successfully fit genomic prediction models. We concluded that for grain yield, the single-environment genomic prediction models examined in this study are equivalent in terms of predictive ability while, in general, multi-environment models that explicitly split marker effects in main and environmental-specific effects outperform simpler multi-environment models.

Functional gene assessment of bread wheat: breeding implications in Ningxia Province

BackgroundThe overall genetic distribution and divergence of cloned genes among bread wheat varieties that have occurred during the breeding process over the past few decades in Ningxia Province, China, are poorly understood. Here, we report the genetic diversities of 44 important genes related to grain yield, quality, adaptation and resistance in 121 Ningxia and 86 introduced wheat cultivars and advanced lines.ResultsThe population structure indicated characteristics of genetic components of Ningxia wheat, including landraces of particular genetic resources, introduced varieties with rich genetic diversities and modern cultivars in different periods. Analysis of allele frequencies showed that the dwarfing alleles Rht-B1b at Rht-B1 and Rht-D1b at Rht-D1, 1BL/1RS translocation, Hap-1 at GW2-6B and Hap-H at Sus2-2B are very frequently present in modern Ningxia cultivars and in introduced varieties from other regions but absent in landraces. This indicates that the introduced wheat germplasm with numerous beneficial genes is vital for broadening the genetic diversity of Ningxia wheat varieties. Large population differentiation between modern cultivars and landraces has occurred in adaptation genes. Founder parents carry excellent allele combinations of important genes, with a higher number of favorable alleles than modern cultivars. Gene flow analysis showed that six founder parents have greatly contributed to breeding improvement in Ningxia Province, particularly Zhou 8425B, for yield-related genes.ConclusionsVarieties introduced from other regions with rich genetic diversity and landraces with well-adapted genetic resources have been applied to improve modern cultivars. Founder parents, particularly Zhou 8425B, for yield-related genes have contributed greatly to wheat breeding improvement in Ningxia Province. These findings will greatly benefit bread wheat breeding in Ningxia Province as well as other areas with similar ecological environments.

Nested Association Mapping (NAM) Populations: Present Status and Future Prospects in the Genomics Era

Development of mapping population is a prerequisite for genetic dissection of genomic regions underlying complex traits. Nested Association Mapping (NAM) is an integrated multi-parent population approach that combines the advantages of linkage mapping and association mapping for high resolution and high-power mapping of complex traits. The NAM population is constituent of independent RIL populations derived from crossing several diverse donor parents with a common founder parent. The first NAM population was developed in maize and later on in several crops like barley, sorghum, wheat, rice, soybean, etc. This review provides an overview of NAM population development, its features, advantages over the other mapping populations, availability of high density genotyping platforms, key considerations for their development, applications and future prospects. We propose that the recent high-throughput analytical tools including high-end genotyping will accelerate utilization of NAM population for prediction of genomic estimated breeding value and genomic assisted selection in crop improvement program.

Strawberry fruit shape: quantification by image analysis and QTL detection by genome-wide association analysis.

Fruit shape of cultivated strawberry (Fragaria × ananassa Duch.) is an important breeding target. To detect genomic regions associated with this trait, its quantitative evaluation is needed. Previously we created a multi-parent advanced-generation inter-cross (MAGIC) strawberry population derived from six founder parents. In this study, we used this population to quantify fruit shape. Elliptic Fourier descriptors (EFDs) were generated from 2 969 two-dimensional binarized fruit images, and principal component (PC) scores were calculated on the basis of the EFD coefficients. PC1–PC3 explained 96% of variation in shape and thus adequately quantified it. In genome-wide association study, the PC scores were used as phenotypes. Genome wide association study using mixed linear models revealed 2 quantitative trait loci (QTLs) for fruit shape. Our results provide a novel and effective method to analyze strawberry fruit morphology; the detected QTLs and presented method can support marker-assisted selection in practical breeding programs to improve fruit shape.

Multiple Genome Wide Association Mapping Models Identify Quantitative Trait Nucleotides for Brown Planthopper (Nilaparvata lugens) Resistance in MAGIC Indica Population of Rice.

Brown planthopper (BPH), one of the most important pests of the rice (Oryza sativa) crop, becomes catastrophic under severe infestations and causes up to 60% yield loss. The highly disastrous BPH biotype in the Indian sub-continent is Biotype 4, which also known as the South Asian Biotype. Though many resistance genes were mapped until now, the utility of the resistance genes in the breeding programs is limited due to the breakdown of resistance and emergence of new biotypes. Hence, to identify the resistance genes for this economically important pest, we have used a multi-parent advanced generation intercross (MAGIC) panel consisting of 391 lines developed from eight indica founder parents. The panel was phenotyped at the controlled conditions for two consecutive years. A set of 27,041 cured polymorphic single nucleotide polymorphism (SNPs) and across-year phenotypic data were used for the identification of marker–trait associations. Genome-wide association analysis was performed to find out consistent associations by employing four single and two multi-locus models. Sixty-one SNPs were consistently detected by all six models. A set of 190 significant marker-associations identified by fixed and random model circulating probability unification (FarmCPU) were considered for searching resistance candidate genes. The highest number of annotated genes were found in chromosome 6 followed by 5 and 1. Ninety-two annotated genes identified across chromosomes of which 13 genes are associated BPH resistance including NB-ARC (nucleotide binding in APAF-1, R gene products, and CED-4) domain-containing protein, NHL repeat-containing protein, LRR containing protein, and WRKY70. The significant SNPs and resistant lines identified from our study could be used for an accelerated breeding program to develop new BPH resistant cultivars.