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Detecting mislabeling and identifying unique progeny in Acacia mapping population using snp markers

Journal of Forestry Research 2017年第6期28卷 1118-1126页

作者： Asif Javed Muhammad Mohd Zaki Abdullah Norwati Muhammad Wickneswari Ratnam Faculty of Science and Technology Universiti Kebangsaan Malaysia 43600 Bangi Selangor Malaysia Forestry Biotechnology Division Forest Research Institute Malaysia 52110 Kepong Selangor Darul Ehsan Malaysia Department of Forestry and Range Management University of Agriculture Faisalabad Faisalabad Pakistan

Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved through marker assisted selection(MAS) breeding. To develop a MAS program requires development of linkage maps and QTL analysis. Two mapping populations were developed through interspecific hybridization for linkage mapping and QTL analysis. All seeds per pod were cultured initially to improve hybrid yield as quality and density of linkage mapping is affected by the size of the mapping population. Progenies from two mapping populations were field planted for phenotypic and genotypic evaluation at three locations in Malaysia,(1) Forest Research Institute Malaysia field station at Segamat, Johor,(2) Borneo Tree Seeds and Seedlings Supplies Sdn, Bhd.(BTS) field trial site at Bintulu, Sarawak, and(3) Asiaprima RCF field trial site at Lancang, Pahang. During field planting, mislabeling was reported at Segamat, Johor, and a similar problem was suspected for Bintulu, Sarawak. Early screening with two isozymes effectively selected hybrid progenies, and these hybrids were subsequently further confirmed by using species-specific snps. During field planting, clonal mislabeling was reported and later confirmed by using a small set of STMS markers. A large set of snps were also used to screen all ramets in both populations. A total of 65.36% mislabeled ramets were encountered in the wood density population and 60.34% in the fibre length mapping population. No interpopulation pollen contamination was detected because all ramets found their match within the same population in ***, mislabeling was detected among ramets of the same population. Mislabeled individuals were identified and grouped as they originated from 93 pods for wood density and 53 pods for fibre length mapping *** average 2 meiotically unique seeds per pod(179 seeds/93 pods) for w

关键词： Tree breeding snp markers Mislabeling Linkage mapping Quantitative trait loci(QTL) mapping

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Genome-wide association analysis of salt tolerance QTLs with snp markers in maize（Zea mays L.）

Genome-wide association analysis of salt tolerance QTLs with...

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2018中国遗传学会第十次全国会员代表大会暨学术讨论会

作者： Yonghong Xie Yan Feng Qi Chen Feike Zhao Shuwei Zhai Ying Ding Baohua Wang Ping Li Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region School of Life SciencesNantong University

In this research, we identified the genotypes of 152 maize inbred lines with high-density chips. Genome-wide association analysis（GWAS） was carried out to identify the significant single nucleotide polymorphisms（snps） which were associated with maize salt tolerance. Totally 34,972 snps with high quality and diversity were selected from 56,110 snp markers, which were distributed on 10 chromosomes of maize. The GLM algorithm in TASSEL was used to analyze the five traits related to salt tolerance. Using a strict LOD threshold of 3.5, totally 46 snp loci were identified which were significantly correlated with plant height change rate, wilting degree, fresh weight change rate, dry weight change rate and comprehensive index respectively. The 46 snp loci were distributed in all chromosomes except for chromosome 10. The high density fingerprints of 152 inbred lines were clustered by TASSEL software to construct genetic clustering map to estimate the genetic distance and the subgroups. The 152 maize inbred lines were divided into two groups: SS group and NSS group, and the snp loci of the salt-tolerant index showed great difference in chromosome distribution. Based on previous studies, we screened 8 candidate genes for salt tolerance in maize and one of them was further validated by real-time quantitative PCR.

关键词： maize inbred line salt-tolerant snp markers association analysis

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Genetic Diversity and Population Structure Analysis of Barley Landraces from Shanghai Region Using Genotyping-by-Sequencing

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Phyton-International Journal of Experimental Botany 2023年第4期92卷 1275-1287页

作者： Luli Li Nigel G.Halford Huihui Wang Yingjie Zong Zhenzhu Guo Ruiju Lu Chenghong Liu Zhiwei Chen Shanghai Key Laboratory of Agricultural Genetics and Breeding Biotechnology Research InstituteShanghai Academy of Agricultural SciencesShanghai201106China College of Fisheries and Life Science Shanghai Ocean UniversityShanghai201306China Rothamsted Research HarpendenAL52JQUK Qingdao OE Biotechnology Company Limited Qingdao266100China

Barley(Hordeum vulgare L.)is an important economic crop for food,feed and industrial raw *** the present research,112 barley landraces from the Shanghai region were genotyped using genotyping-by-sequencing(GBS),and the genetic diversity and population structure were *** results showed that 210,268 Single Nucleotide Polymorphisms(snps)were present in total,and the average poly-morphism information content(PIC)was *** diversity and population structure analyses suggested that these barley landraces were differentiated and could be divided into three sub-groups,with morphological traits of row-type and adherence of the hulls the main distinguishing factors between *** with similar or duplicated names were also investigated according to their genetic backgrounds and seed *** study provided valuable information on barley landraces from the Shanghai region,and showed that all these barley landraces should be protected and used for future breeding programs.

关键词： Hordeum vulgare L cluster analysis population structure snp markers

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Genome-wide association studies reveal QTL hotspots for grain brightness and black point traits in barley

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The Crop Journal 2021年第1期9卷 154-167页

作者： Yong Jia Sharon Westcott Tianhua He Lee Anne McFawn Tefera Angessa Camila Hill Cong Tan Xiaoqi Zhang Gaofeng Zhou Chengdao Li Western Barley Genetics Alliance MurdochWA 6150Australia State Agricultural Biotechnology Centre(SABC) Murdoch UniversityMurdochWA 6150Australia Department of Primary Industries and Regional Development South PerthWA 6151Australia China National GeneBank Shenzhen 518120GuangdongChina

Grain kernel discoloration(KD)in cereal crops leads to down-grading grain quality and substantial economic losses *** KD tolerant varieties requires a clear understanding of the genetic basis underlying this ***,we generated a high-density single nucleotide polymorphisms(snps)map for a diverse barley germplasm and collected trait data from two independent field trials for five KD related traits:grain brightness(TL),redness(Ta),yellowness(Tb),black point impact(Tbpi),and total black point in percentage(Tbpt).Although grain brightness and black point is genetically correlated,the grain brightness traits(TL,Ta,and Tb)have significantly higher heritability than that of the black point traits(Tbpt and Tbpi),suggesting black point traits may be more susceptible to environmental *** genome-wide association studies(GWAS),we identified a total of 37 quantitative trait loci(QTL),including two major QTL hotspots on chromosomes 4H and 7H,*** two QTL hotspots are associated with all five KD *** genetic linkage and gene transcription analyses identified candidate genes for the grain KD,including several genes in the flavonoid pathway and plant *** study provides valuable insights into the genetic basis for the grain KD in barley and would greatly facilitate future breeding programs for improving grain KD resistance.

关键词： Barley Black point Grain brightness GWAS Kernel discoloration snp markers

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Identification of Putative Qtls Associated with Maize Kernel Length Using Double Haploid Lines

Identification of Putative Qtls Associated with Maize Kernel...

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作者： GHULAM AISHIA 华中农业大学

学位级别：硕士

Maize(Zea mays L.) is one of the most prominent cereal crops playing a crucial role in sustaining global food security. In breeding programs, grain size characters including kernel length(KL), kernel width and kernel thickness are importantly considered for the evaluation of kernel weight. The KL was reported to be significantly and positively correlated with the kernel size or/and kernel weight, as well as the final grain yield of maize. In the present study, the haploid lines derived from the intermated B73×Mo17 Syn 10 doubled haploid(IBM Syn10) mapping population were used to identify the putative QTLs for KL in different agroecological environments and to understand the stability of QTL across environment. The linkage map, consists of 6540 markers, with an average chromosome length of 1113.6 came were used for QTL mapping. The major findings of the present experiment are summarized below.1. Phenotypic data revealed that maize KL varied significantly under the main effect as well as the interaction of different environments and DH lines. Under all the environments, the average KL of DH lines was quantitatively higher than their parents, suggesting the efficacy of intermating for ten generations. Higher broad sense heritability(0.89) and lower kurtosis as well as scenes values(2.5) associated with KL, among these 12 and 24 QTLs were specifically identified in Heilongjiang and Yunnan environments, respectively. All the identified QTLs were well distributed over all the 10 maize chromosomes. Seven putative QTLs were found on chromosome 1 and 8, six QTLs on chromosome 2, and three QTLs for each on chromosome 6, 9 and 10. Only one QTL was observed on chromosome 4 as well as chromosome 5, while two

关键词： double haploid maize kernel length QTL detection snp markers

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Mapping Qtls for Grain Yield and Yield Components in Kenyan Maize (<i>Zea mays</i>L.) Under Low Phosphorus Using Single Nucleotide Polymorphism (snpS)

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American Journal of Plant Sciences 2021年第7期12卷 1106-1123页

作者： Evans Ochieng Ouma Gudu Samuel Rongo University Rongo Kenya

Selection for tolerance to low phosphorus (P) using morphological traits alone is slow and often confounded by environmental effects. This study identified some Quantitative Trait Loci (QTLs) associated with grain yield (GYLD), Plant (PHT) and Ear heights (EHT) under low P in maize using single nucleotide polymorphic markers. 228 F2:3 individuals derived from a cross between two contrasting maize inbred lines together with 239 SNPs were mapped onto ten linkage groups (LGs) spanning 2255 centiMorgans (cM) with an average inter-marker distance of 9.44 cM. Majority of the SNP markers (63%) followed the Mendelian segregation and were fairly distributed in all the LGs. Mean performance for all the traits in the F3 population was higher than the parental values, which suggested transgressive segregation for all traits. Low to moderate broad sense heritability (0.35 - 0.50) in the F3 population for GYLD, PHT and EHT indicated that tolerance to low P is controlled by complex multi genetic factors. A full multi-QTL model analysis suggested six QTLs (2 QTLs each for GYLD, PHT and EHT) located on chromosomes 1, 3, 4 and 8. The two QTLs for GYLD increased maize yield under low P soils by 173 kg/ha while the 2 QTLs for PHT increased plant growth by 18.14 cm. The % phenotypic variance explained by these QTLs under low P environments had a wide range (0.242% - 53.34%) and was much lower for GYLD compared to plant growth. Both additive and dominance gene actions contributed differentially to the observed phenotypic variance for tolerance to low P soils with domin

关键词： snp markers Additive Dominance Heritability Low P Maize QTLs

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Genetic Structure and Diversity Study of Cassava (Manihot esculenta) Germplasm for African Cassava Mosaic Disease and Fresh Storage Root Yield

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Open Journal of Genetics 2023年第1期13卷 23-47页

作者： Janatu Veronica Sesay Aiah Lebbie Richard Wadsworth Ephraim Nuwamanya Souleymane Bado Prince Emmanuel Norman Sierra Leone Agricultural Research Institute PMB 1313 Tower Hill Freetown Sierra Leone Department of Biological Sciences School of Environmental Sciences Njala University Njala Sierra Leone Makerere University Kampala Kampala Uganda Department of Plant Science Phytoprise GmbH DI Rudolf Schober-StraBe 4 7400 Oberwart Oberwart Austria

A better understanding of population structure and genetic diversity among cassava germplasm for African cassava mosaic disease and fresh root yield traits is useful for cassava improvement programme. Phenotype-based selection for these traits is cumbersome due to phenotypic plasticity and difficulty in screening of phenotypic-induced variations. This study assessed quantitative trait loci (QTL) regions associated with African cassava mosaic disease (ACMD) and fresh storage root yield (FSRY) in 131 cassava (Manihot esculenta) genotypes using a genome-wide association study (GWAS). The single nucleotide polymorphism (snp) loci and associated candidate genes, when validated, would be a valuable resource for marker-assisted selection in the breeding process for development of new cassava genotypes with improved resistance to ACMD and desirable high root yield. Population structure analysis using 12,500 snps differentiated the 131 genotypes into five distinct sub-groups (K = 5). Marker-trait association (MTA) analysis using the generalized linear model identified two QTL regions significant for ACMD and three for FSRY. This study demonstrated that DArTseq markers are useful genomic resources for genome-wide association studies of ACMD and FSRY traits in cassava for the acceleration of varietal development and release.

关键词： Population Structure Genetic Variability GWAS snp markers Cassava

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Transcriptome analysis differentially expressed genes with total carotenoid contents in pearl oyster(Pinctada fucata martensii)

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Marine Science Bulletin 2022年第1期24卷 56-71页

作者： LIU Yong YANG Xiuyan LEI Chao LI Junhui YANG Chuangye DENG Yuewen Fisheries College Guangdong Ocean UniversityZhanjiang 524088China Pearl Breeding and Processing Engineering Technology Research Center of Guangdong Province Zhanjiang 524088China Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding Zhanjiang 524088China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture Zhanjiang 524088China

Differentially expressed genes(DEGs)between individuals with high(HC)and low(LC)total carotenoid content(TCC)were sampled from a selected line of Pinctada fucata martensii with black shell in the prismatic *** expression levels of candidate genes were verified by *** resequencing was used to detect snps in a candidate gene,*** association of TCC with snps in PmSR-BI was *** showed that a total of 1025 DEGs were identified between HC and *** expression levels of the candidate gene PmSR-BI in HC were higher than those in *** snps in the exon and eight snps in the 5′regulatory regions of PmSR-BI were *** analysis showed that one snp in the exon and two snps in the 5′regulatory regions of PmSR-BI were significantly associated with the TCC(Psnps of PmSR-BI were divided into four *** haplotype in Block 1 and AG haplotype in Block 3 were significantly higher than other *** results help elucidate the mechanism underlying carotenoid metabolism and develop marker-assisted breeding design in the species.

关键词： Pinctada fucata martensii Total carotenoid content Scavenger Receptors Class B Type Ⅰ snp markers

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