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Molecular Breeding: New Strategies in Plant Improvement

Roeland E Voorrips, Marco C A M Bink, Johannes W Kruisselbrink, Herma J J Koehorst-van Putten, W Eric van de Weg
In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called "haploblocks". Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time...
2016: Molecular Breeding: New Strategies in Plant Improvement
Yansong Ma, Jochen C Reif, Yong Jiang, Zixiang Wen, Dechun Wang, Zhangxiong Liu, Yong Guo, Shuhong Wei, Shuming Wang, Chunming Yang, Huicai Wang, Chunyan Yang, Weiguo Lu, Ran Xu, Rong Zhou, Ruizhen Wang, Zudong Sun, Huaizhu Chen, Wanhai Zhang, Jian Wu, Guohua Hu, Chunyan Liu, Xiaoyan Luan, Yashu Fu, Tai Guo, Tianfu Han, Mengchen Zhang, Bincheng Sun, Lei Zhang, Weiyuan Chen, Cunxiang Wu, Shi Sun, Baojun Yuan, Xinan Zhou, Dezhi Han, Hongrui Yan, Wenbin Li, Lijuan Qiu
Genomic selection is a promising molecular breeding strategy enhancing genetic gain per unit time. The objectives of our study were to (1) explore the prediction accuracy of genomic selection for plant height and yield per plant in soybean [Glycine max (L.) Merr.], (2) discuss the relationship between prediction accuracy and numbers of markers, and (3) evaluate the effect of marker preselection based on different methods on the prediction accuracy. Our study is based on a population of 235 soybean varieties which were evaluated for plant height and yield per plant at multiple locations and genotyped by 5361 single nucleotide polymorphism markers...
2016: Molecular Breeding: New Strategies in Plant Improvement
Sanjaya Gyawali, Myrtle Harrington, Jonathan Durkin, Kyla Horner, Isobel A P Parkin, Dwayne D Hegedus, Diana Bekkaoui, Lone Buchwaldt
The fungal pathogen Sclerotinia sclerotiorum causes stem rot of oilseed rape (Brassica napus) worldwide. In preparation for genome-wide association mapping (GWAM) of sclerotinia resistance in B. napus, 152 accessions from diverse geographical regions were screened with a single Canadian isolate, #321. Plants were inoculated by attaching mycelium plugs to the main stem at full flower. Lesion lengths measured 7, 14 and 21 days after inoculation were used to calculate the area under the disease progress curve (AUDPC)...
2016: Molecular Breeding: New Strategies in Plant Improvement
Weijun Ye, Shikai Hu, Liwen Wu, Changwei Ge, Yongtao Cui, Ping Chen, Xiaoqi Wang, Jie Xu, Deyong Ren, Guojun Dong, Qian Qian, Longbiao Guo
Chloroplast is a crucial organelle for plant photosynthesis and maintaining normal life activities in higher plants. Although some genes related to chloroplast development and pigment synthesis have been identified or cloned in rice, little is known about the relationship between these genes and abiotic stress response. In this study, we identified a novel mutant white stripe leaf 12 (wsl12) affecting pigment synthesis, chloroplast development and abiotic stress response in rice. The mutant phenotype was obvious at seeding and tillering stages and in response to the temperature change...
2016: Molecular Breeding: New Strategies in Plant Improvement
Bjarne Larsen, Marian Ørgaard, Torben Bo Toldam-Andersen, Carsten Pedersen
We present a new efficient screening tool for detection of S-alleles in apple. The protocol using general and multiplexed primers for PCR reaction and fragment detection on an automatized capillary DNA sequencer exposed a higher number of alleles than any previous studies. Analysis of alleles is made on basis of three individual fragment sizes making the allele interpretation highly accurate. The method was employed to genotype 432 Malus accessions and exposed 25 different S-alleles in a selection of Malus domestica cultivars of mainly Danish origin (402 accessions) as well as a selection of other Malus species (30 accessions)...
2016: Molecular Breeding: New Strategies in Plant Improvement
Yongli Zhao, Chong Zhang, Hua Chen, Mei Yuan, Rick Nipper, C S Prakash, Weijian Zhuang, Guohao He
Bacterial wilt (BW) caused by Ralstonia solanacearum is a serious, global, disease of peanut (Arachis hypogaea L.), but it is especially destructive in China. Identification of DNA markers linked to the resistance to this disease will help peanut breeders efficiently develop resistant cultivars through molecular breeding. A F2 population, from a cross between disease-resistant and disease-susceptible cultivars, was used to detect quantitative trait loci (QTL) associated with the resistance to this disease in the cultivated peanut...
2016: Molecular Breeding: New Strategies in Plant Improvement
Claire Lessa Alvim Kamei, Edouard I Severing, Annemarie Dechesne, Heleen Furrer, Oene Dolstra, Luisa M Trindade
Many important crops have received little attention by the scientific community, either because they are not considered economically important or due to their large and complex genomes. De novo transcriptome assembly, using next-generation sequencing data, is an attractive option for the study of these orphan crops. In spite of the large amount of sequencing data that can be generated, there is currently a lack of tools which can effectively help molecular breeders and biologists to mine this type of information...
2016: Molecular Breeding: New Strategies in Plant Improvement
Dorota Sołtys-Kalina, Katarzyna Szajko, Izabela Sierocka, Jadwiga Śliwka, Danuta Strzelczyk-Żyta, Iwona Wasilewicz-Flis, Henryka Jakuczun, Zofia Szweykowska-Kulinska, Waldemar Marczewski
Potato (Solanum tuberosum L.) tubers exhibit significant variation in reducing sugar content directly after harvest, cold storage and reconditioning. Here, we performed QTL analysis for chip color, which is strongly influenced by reducing sugar content, in a diploid potato mapping population. Two QTL on chromosomes I and VI were detected for chip color after harvest and reconditioning. Only one region on chromosome VI was linked with cold-induced sweetening. Using the RT-PCR technique, we showed differential expression of the auxin-regulated protein (AuxRP) gene...
2015: Molecular Breeding: New Strategies in Plant Improvement
Cancan Wang, Chuanrong Li, Charles A Leslie, Qingrong Sun, Xianfeng Guo, Keqiang Yang
Tocopherol cyclase (VTE1) plays a key role in promoting the production of γ-tocopherol and improving total tocopherol content in photosynthetic organisms. Walnut is an important source of tocopherols in the human diet, and γ-tocopherol is the major tocopherol compound in walnut kernels. In this study, a full-length cDNA of the VTE1 gene was isolated from walnut using RT-PCR and RACE, and designated as JrVTE1. The full-length cDNA of the JrVTE1 gene contained a 1353-bp open-reading frame encoding a 451-amino-acid protein with a calculated molecular weight of 49...
2015: Molecular Breeding: New Strategies in Plant Improvement
Agnieszka Niedziela, Dariusz Mańkowski, Piotr T Bednarek
The tolerance of triticale (x Triticosecale Wittmack) cultivars to aluminum (Al) stress observed in acid soils is an important agronomic trait affecting seed yield. Traditionally, breeding of Al-tolerant cultivars was selection based; for example, using a physiological test. However, such selection methods are relatively slow and require numerous plants for phenotype evaluation. Alternatively, DNA-based molecular marker systems could be applied to identify markers useful for selection purposes. Among many marker platforms available, Diversity Arrays Technology (DArT) is one of the most promising...
2015: Molecular Breeding: New Strategies in Plant Improvement
Xiaochun Sun, Rita H Mumm
Multiple trait integration (MTI) is the process by which a target hybrid (or variety) is converted to add value-added traits to the comprehensive performance package represented by that genotype. The goal is to recover all the attributes of the target hybrid, with the addition of the specified value-added traits. In maize, this process utilizes the backcross breeding method to incorporate transgenic events (or genes) of interest. Thus, MTI involves four main steps: single event introgression, event pyramiding, trait fixation, and version testing to ensure recovery of equivalent performance with at least one version of the converted hybrid...
2015: Molecular Breeding: New Strategies in Plant Improvement
Yi Ren, Di Jiao, Guoyi Gong, Haiying Zhang, Shaogui Guo, Jie Zhang, Yong Xu
Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. niveum (FON) is the major soilborne disease of watermelon (Citrullus lanatus L.). The development and deployment of resistant cultivars is generally considered to be an effective approach to control FW. In this study, an F8 population consisting of 103 recombinant inbred lines derived from a cross between the cultivar 97103 and a wild accession PI 296341-FR was used for FON race 1 and race 2 fungal inoculations. One major QTL on chromosome 1 for FON race 1 resistance was detected with a logarithm of odds of 13...
2015: Molecular Breeding: New Strategies in Plant Improvement
G R A Margarido, M M Pastina, A P Souza, A A F Garcia
Breeding trials typically consist of phenotypic observations for various traits evaluated in multiple environments. For sugarcane in particular, repeated measures are obtained for plant crop and one or more ratoons, such that joint analysis through mixed models for modeling heterogeneous genetic (co)variances between traits, locations and harvests is appropriate. This modeling approach also enables us to include molecular marker information, aiding in understanding the genetic architecture of quantitative traits...
2015: Molecular Breeding: New Strategies in Plant Improvement
Marty J Faville, Lyn Briggs, Mingshu Cao, Albert Koulman, M Z Zulfi Jahufer, John Koolaard, David E Hume
The association between perennial ryegrass (Lolium perenne L.) and its Epichloë fungal endophyte symbiont, Epichloë festucae var. lolii, supports the persistence of ryegrass-based pastures principally by producing bioactive alkaloid compounds that deter invertebrate herbivory. The host plant genotype affects endophyte trait expression, and elucidation of the underlying genetic mechanisms would enhance understanding of the symbiosis and support improvement of in planta endophyte performance through plant breeding...
2015: Molecular Breeding: New Strategies in Plant Improvement
Li Liu, Daniel Jeffers, Yudong Zhang, Meiling Ding, Wei Chen, Manjit S Kang, Xingming Fan
Quality protein maize (QPM; Zea mays L.) has effectively enhanced levels of the amino acids, lysine, and tryptophan, over normal maize and provided balanced dietary protein for the health and development of monogastric animals and humans. However, as in normal maize, QPM varieties are low in provitamin A (ProVA), a precursor of vitamin A, which can lead to vitamin A deficiency in humans when maize is a significant part of their diet. In this study, maize inbred Hp321-1 carrying the favorable alleles crtRB1-5'TE-2 and crtRB1-3'TE-1 that can enhance levels of ProVA, was used as donor for improving ProVA in QPM inbred lines CML161 and CML171...
2015: Molecular Breeding: New Strategies in Plant Improvement
Xuehui Feng, Don Keim, Humphrey Wanjugi, Issa Coulibaly, Yan Fu, John Schwarz, Scott Huesgen, Seungho Cho
Genetic male sterility (GMS) in cotton mediated by two homozygous recessive genes, ms5ms5 and ms6ms6, is expressed as non-dehiscent anthers and unviable pollen grains. Sequence analysis on ms5 and ms6 loci in Gossypium hirsutum was conducted to reveal genomic variation at these two loci between GMS and wild-type G. hirsutum inbred lines, and sequence polymorphism linked to ms5 on A12 and ms6 on D12 was revealed. A haplotype marker set that consisted of four SNPs targeting both ms5 and ms6 gene regions was developed and validated for association with GMS in cotton...
2015: Molecular Breeding: New Strategies in Plant Improvement
Manish L Raorane, Isaiah M Pabuayon, Berta Miro, Rajesh Kalladan, Mohammad Reza-Hajirezai, Rowena H Oane, Arvind Kumar, Nese Sreenivasulu, Amelia Henry, Ajay Kohli
There is a widespread consensus that drought will mostly affect present and future agriculture negatively. Generating drought-tolerant crops is thus a high priority. However complicated the underlying genetic and regulatory networks for differences in plant performance under stress are, they would be reflected in straightforward differences in primary metabolites. This is because primary metabolites such as amino acids and sugars form the building blocks of all pathways and processes for growth, development, reproduction, and environmental responses...
2015: Molecular Breeding: New Strategies in Plant Improvement
Hong-Li Tian, Feng-Ge Wang, Jiu-Ran Zhao, Hong-Mei Yi, Lu Wang, Rui Wang, Yang Yang, Wei Song
Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the maize (Zea mays L.) genome. SNPs have several advantages over simple sequence repeats, such as ease of data comparison and integration, high-throughput processing of loci, and identification of associated phenotypes. SNPs are thus ideal for DNA fingerprinting, genetic diversity analysis, and marker-assisted breeding. Here, we developed a high-throughput and compatible SNP array, maizeSNP3072, containing 3072 SNPs developed from the maizeSNP50 array...
2015: Molecular Breeding: New Strategies in Plant Improvement
Myluska Caro, Maarten G Verlaan, Olga Julián, Richard Finkers, Anne-Marie A Wolters, Samuel F Hutton, John W Scott, Richard Kormelink, Richard G F Visser, Maria J Díez, Ana Pérez-de-Castro, Yuling Bai
Tomato yellow leaf curl virus (TYLCV) hampers tomato production worldwide. Our previous studies have focussed on mapping and ultimately cloning of the TYLCV resistance genes Ty-1 and Ty-3. Both genes are derived from Solanum chilense and were shown to be allelic. They code for an RNA-dependent RNA polymerase (RDR) belonging to the RDRγ type defined by a DFDGD catalytic domain. In this study, we first fine-mapped the TYLCV resistance in S. chilense LA1932, LA1960 and LA1971. Results showed that chromosomal intervals of the causal genes in these TYLCV-resistant accessions overlap and cover the region where Ty-1/Ty-3 is located...
2015: Molecular Breeding: New Strategies in Plant Improvement
Yongqing Jiao, Tri D Vuong, Yang Liu, Zenglu Li, Jim Noe, Robert T Robbins, Trupti Joshi, Dong Xu, J Grover Shannon, Henry T Nguyen
Soybean cyst nematode (SCN, Heterodera glycine Ichinohe), southern root-knot nematode [SRKN, Meloidogyne incognita (Kofoid and White) Chitwood] and reniform nematode (RN, Rotylenchulus reniformis Linford and Oliveira) are three important plant-parasitic pests in soybean. Previous study showed that plant introduction (PI) 567516C harbored novel quantitative trait loci (QTL) conferring SCN resistance to soybean. However, QTL underlying resistance to SRKN and RN in PI 567516C remain unknown. The objectives of this study were to identify QTL for resistance to SRKN and RN in PI 567516C...
2015: Molecular Breeding: New Strategies in Plant Improvement
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