Challenges for QTL Analysis in Crops

Yan Long,Chunyu Zhang,Jinling Meng 한국작물학회 2008 Journal of crop science and biotechnology Vol.11 No.1

Quantitative trait loci, a genetic concept introduced in the 1940s, for explaining the inheritance of non-Mendelian traits, have been realized as particular fragments of chromosomes even unique genes in most crops in the 21st century. However, only very a small portion of QTL has been screened out by geneticists comparing to a great number of genes underneath the quantitative traits. These identified QTL even have been seldom used into breeding program because crop breeders may not find the QTL in their breeding populations in their field station. Several key points will be proposed to meet the challenges of QTL analysis today: a fine mapping population and the related reference genetic map, QTL evaluation in multiple environments, recognizing real QTL with small genetic effect, map integration. Quantitative trait loci, a genetic concept introduced in the 1940s, for explaining the inheritance of non-Mendelian traits, have been realized as particular fragments of chromosomes even unique genes in most crops in the 21st century. However, only very a small portion of QTL has been screened out by geneticists comparing to a great number of genes underneath the quantitative traits. These identified QTL even have been seldom used into breeding program because crop breeders may not find the QTL in their breeding populations in their field station. Several key points will be proposed to meet the challenges of QTL analysis today: a fine mapping population and the related reference genetic map, QTL evaluation in multiple environments, recognizing real QTL with small genetic effect, map integration.

Challenges for QTL Analysis in Crops

Long, Yan,Zhang, Chunyu,Meng, Jinling The Korean Society of Crop Science 2008 Journal of crop science and biotechnology Vol.11 No.1

Quantitative trait loci, a genetic concept for explaining the inheritance of non-Mendelian traits in 1940s, have been realized as particular fragments of chromosome even unique genes in most crops in 21st century. However, only very a small portion of QTL has been screened out by geneticists comparing to a great number of genes underneath the quantitative traits. These identified QTL even have been seldom used into breeding program because crop breeders may not find the QTL in their breeding populations in their field station. Several key points will be proposed to meet the challenges of QTL analysis today: a fine mapping population and the related reference genetic map, QTL evaluation in multiple environments, recognizing real QTL with small genetic effect, map integration.

Genetic Diversity of Brassica Species Revealed by Amplified Fragment Length Polymorphism and Simple Sequence Repeat Markers

Maoteng Li,Chunyu Zhang,Wei Qian,Jinling Meng 한국원예학회 2007 Horticulture, Environment, and Biotechnology Vol.48 No.1

Amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers were employed for assessing the genetic diversity of 21 Brassica cultivars including three oilseed species, B. rapa, B. carinata, and B. napus. Nineteen AFLP primer pairs generated an average of 83.05 with 78.95 polymorphic bands (95.05% of polymorphism) and 19 SSR primer pairs produced an average of 11.16 allelic products with 10.74 polymorphic products (91.50% of polymorphism). The dendrogram showed that the three species can be clearly distinguished and every two B. rapa cultivars was with the most abundant genetic diversity. The similarity matrixes detected by two-way Mantel test showed that the matrix correlation between the data from 19 AFLP and 19 SSR primer pairs showed a good fit, which revealed that the AFLP and SSR markers were all good for assessing the genetic diversity of Brassica species. However, the AFLP markers had slightly higher resolution of genetic similarities than the SSR markers.

Retrotransposons- a Major Driving Force in Plant Genome Evolution and a Useful Tool for Genome Analysis

Jun Zou,Huihui Gong,Tae-Jin Yang,Jinling Meng 한국작물학회 2009 Journal of crop science and biotechnology Vol.12 No.1

As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to the unforeseen transposition activities. Regulation of transposition is relatively complex and three factors such as maintaining structure for none- or cis- or trans-acting transposition, control by host genome and induction by biotic and abiotic stress may contribute altering its transposition activity. The important roles of retrotransposons to modify genome size, remodel genome structure, and displace gene functions in the plant genome have been proven by a growing number of research studies up to now, which indicates that retrotransposons are a great driving force in genome evolution. For this review, we summarized the latest theoretic and practical research progress on plant retrotransposons for their distribution, regulation of activity, the impact on the architecture of plant genomes, and put forward the future prospects. As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to the unforeseen transposition activities. Regulation of transposition is relatively complex and three factors such as maintaining structure for none- or cis- or trans-acting transposition, control by host genome and induction by biotic and abiotic stress may contribute altering its transposition activity. The important roles of retrotransposons to modify genome size, remodel genome structure, and displace gene functions in the plant genome have been proven by a growing number of research studies up to now, which indicates that retrotransposons are a great driving force in genome evolution. For this review, we summarized the latest theoretic and practical research progress on plant retrotransposons for their distribution, regulation of activity, the impact on the architecture of plant genomes, and put forward the future prospects.

Comparative QTL Mapping of Economically Important Traits in Cultivated Brassicas

Nirala Ramchiary,Xiaonan Li,Concong Jiang,Jinling Meng,Chaofan Zhu,Su Ryun Choi,Yong Pyo Lim 한국원예학회 2011 한국원예학회 학술발표요지 Vol.2011 No.5

Retrotransposons - a Major Driving Force in Plant Genome Evolution and a Useful Tool for Genome Analysis

Zou, Jun,Gong, Huihui,Yang, Tae-Jin,Meng, Jinling 한국작물학회 2009 Journal of crop science and biotechnology Vol.12 No.1

As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities. Regulation of transposition is relatively complex and three factors such as maintaining structure for none- or cis- or trans-acting transposition, being controlled by the host genome and induction by biotic and abiotic stress may contribute altering its transposition activity. The important roles of retrotransposons to modify genome size, remodel genome structure, and displace gene functions in the plant genome have been proven by a growing number of research studies till date, which indicates that retrotransposons are important driving force in genome evolution. For this review, we summarized the latest theoretic and practical research progresses on plant retrotransposons for their distribution, regulation of activity, the impact on the architecture of plant genomes, and put forward the future prospects.

Transcriptionally and Phylogenetically Analyzing the P Protein Gene of Glycine Decarboxylase for Understanding the Evolution of C_3-C_4 Species in Brassicaceae

Chunyu Zhang,박인애,Fangsen Xu,Maoteng Li,임용표,Jinling Meng 한국원예학회 2011 Horticulture, Environment, and Biotechnology Vol.52 No.4

Lacking P protein of glycine decarboxylase (GDCP) from the mesophyll cells was one of the major steps for C_3species to evolve into C_3-C_4 species. Previous studies indicated that the lack of P protein in the mesophyll cells of C_3-C_4species of Flaveria is regulated by gene different transcription. In the family of Brassicaceae, most plants show a typical C_3photosynthetic characteristic, which includes some important vegetables and oil crops, while few plants in this family exhibit a C_3-C_4 type of character. To understand the mechanism of difference in distribution of P protein between the 2 different photosynthetic types, a C_3 type of 1.6 kb BnGDCP promoter from Brassica napus was used for detailed analysis in this study. This promoter exhibited the ability to drive beta-glucuronidase gene (GUS) expression in both mesophyll and the bundle sheath cells of C_3 species, Arabidopsis. However, the same promoter was also found to drive GUS expression in both the mesophyll and bundle sheath cells of a typical of C_3-C_4 species such as Moricandia arvensis, which loses the P protein from the mesophyll cells. This implies that in absence of P protein from the mesophyll cells of Moricandia (C_3-C_4 species) may be regulated by differential transcription of the P protein gene as well. And then, a region, which determines a mesophyll cells specific expression, was narrowed down to 135 bp in length through detailed promoter/reporter gene assay. DNA sequences alignment of the 5′-flanking sequences from either a C3 or C_3-C_4 species in Brassicaceae indicated that 2 different nucleotide acids only conserved to C_3 species were revealed. Phylogenetic analysis of those 5′-flanking sequences of GDCP indicated that C_3-C_4 species in the genus of Moricandia might have been evolved from different C_3 ancestors; interestingly, a C_3-C_4species, D. tenuifolia, was indicated to have shared common ancestors with the C_3-C_4 species, M. spinosa, and the C_3 species M. foleyii in Moricandia.

Structural and functional comparative mapping between the Brassica A genomes in allotetraploid Brassica napus and diploid Brassica rapa.

Jiang, Congcong,Ramchiary, Nirala,Ma, Yongbiao,Jin, Mina,Feng, Ji,Li, Ruiyuan,Wang, Hao,Long, Yan,Choi, Su Ryun,Zhang, Chunyu,Cowling, Wallace A,Park, Beom Seok,Lim, Yong Pyo,Meng, Jinling Springer 2011 TAG. Theoretical and applied genetics. Theoretisch Vol.123 No.6

<P>Brassica napus (AACC genome) is an important oilseed crop that was formed by the fusion of the diploids B. rapa (AA) and B. oleracea (CC). The complete genomic sequence of the Brassica A genome will be available soon from the B. rapa genome sequencing project, but it is not clear how informative the A genome sequence in B. rapa (A(r)) will be for predicting the structure and function of the A subgenome in the allotetraploid Brassica species B. napus (A(n)). In this paper, we report the results of structural and functional comparative mapping between the A subgenomes of B. napus and B. rapa based on genetic maps that were anchored with bacterial artificial chromosomes (BACs)-sequence of B. rapa. We identified segmental conservation that represented by syntenic blocks in over one third of the A genome; meanwhile, comparative mapping of quantitative trait loci for seed quality traits identified a dozen homologous regions with conserved function in the A genome of the two species. However, several genomic rearrangement events, such as inversions, intra- and inter-chromosomal translocations, were also observed, covering totally at least 5% of the A genome, between allotetraploid B. napus and diploid B. rapa. Based on these results, the A genomes of B. rapa and B. napus are mostly functionally conserved, but caution will be necessary in applying the full sequence data from B. rapa to the B. napus as a result of genomic rearrangements in the A genome between the two species.</P>

<i>De novo</i> genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of <i>Brassica napus</i> derived from interspecific hybridization with <i>Brassica rapa</i>

Zou, Jun,Fu, Donghui,Gong, Huihui,Qian, Wei,Xia, Wei,Pires, J. Chris,Li, RuiYuan,Long, Yan,Mason, Annaliese S.,Yang, Tae‐,Jin,Lim, Yong P.,Park, Beom S.,Meng, Jinling Blackwell Publishing Ltd 2011 The Plant journal Vol.68 No.2

<P><B>Summary</B></P><P>Interspecific hybridization is a significant evolutionary force as well as a powerful method for crop breeding. Partial substitution of the AA subgenome in <I>Brassica napus</I> (A<SUP>n</SUP>A<SUP>n</SUP>C<SUP>n</SUP>C<SUP>n</SUP>) with the <I>Brassica rapa</I> (A<SUP>r</SUP>A<SUP>r</SUP>) genome by two rounds of interspecific hybridization resulted in a new introgressed type of <I>B.?napus</I> (A<SUP>r</SUP>A<SUP>r</SUP>C<SUP>n</SUP>C<SUP>n</SUP>). In this study, we construct a population of recombinant inbred lines of the new introgressed type of <I>B.?napus</I>. Microsatellite, intron‐based and retrotransposon markers were used to characterize this experimental population with genetic mapping, genetic map comparison and specific marker cloning analysis. Yield‐related traits were also recorded for identification of quantitative trait loci (QTLs). A remarkable range of novel genomic alterations was observed in the population, including simple sequence repeat (SSR) mutations, chromosomal rearrangements and retrotransposon activations. Most of these changes occurred immediately after interspecific hybridization, in the early stages of genome stabilization and derivation of experimental lines. These novel genomic alterations affected yield‐related traits in the introgressed <I>B.?napus</I> to an even greater extent than the alleles alone that were introgressed from the A<SUP>r</SUP> subgenome of <I>B.?rapa</I>, suggesting that genomic changes induced by interspecific hybridization are highly significant in both genome evolution and crop improvement.</P>