Molecular breeding

About: Molecular breeding is a research topic. Over the lifetime, 2120 publications have been published within this topic receiving 56908 citations.

De novo sequencing and characterization of seed transcriptome of the tree legume Millettia pinnata for gene discovery and SSR marker development

Abstract: Pongamia (Millettia pinnata) is a promising biofuel crop with multiple merits. Breeding of ideal Pongamia germplasm for industrial application demands substantial progress in molecular biology of this legume species, which has been largely hampered by the paucity of its genomic data. In this study, we constructed and characterized a comprehensive seed transcriptome by the high-throughput Illumina sequencing technology. We obtained over 83 million high-quality reads, which were processed and assembled into 53,586 unigenes with a mean length of 787 bp. Among these unigenes, 39,602 (73.90 %) and 24,078 (44.93 %) showed significant similarity to proteins in the NCBI non-redundant and the Swiss-Prot protein databases, respectively. Of the annotated unigenes, 30,619 (57.14 %) were classified into 56 Gene Ontology categories. Furthermore, 21,905 (40.88 %) unigenes were assigned to 128 pathways in the Kyoto Encyclopedia of Genes and Genomes pathway database. A set of 364 unigenes involved in five pathways closely related to oil biosynthesis and accumulation were screened out as candidates for future functional analyses. On the other hand, 5710 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified in 4951 unigenes with a density of one SSR every 7.39-kb sequence. One hundred EST-SSRs were randomly selected to validate amplification and to assess polymorphism among 12 Pongamia individuals. Eighty-two primer pairs successfully amplified DNA fragments and 17 of them detected polymorphism, in which the polymorphism information content values ranged from 0.14 to 0.57. This transcriptome dataset will serve as a valuable basis for studies on functional genomics, molecular genetics and molecular breeding of Pongamia.

Root Adaptation via Common Genetic Factors Conditioning Tolerance to Multiple Stresses for Crops Cultivated on Acidic Tropical Soils.

Abstract: Crop tolerance to multiple abiotic stresses has long been pursued as a Holy Grail in plant breeding efforts that target crop adaptation to tropical soils. On tropical, acidic soils, aluminum (Al) toxicity, low phosphorus (P) availability and drought stress are the major limitations to yield stability. Molecular breeding based on a small suite of pleiotropic genes, particularly those with moderate to major phenotypic effects, could help circumvent the need for complex breeding designs and large population sizes aimed at selecting transgressive progeny accumulating favorable alleles controlling polygenic traits. The underlying question is twofold: do common tolerance mechanisms to Al toxicity, P deficiency and drought exist? And if they do, will they be useful in a plant breeding program that targets stress-prone environments. The selective environments in tropical regions are such that multiple, co-existing regulatory networks may drive the fixation of either distinctly different or a smaller number of pleiotropic abiotic stress tolerance genes. Recent studies suggest that genes contributing to crop adaptation to acidic soils, such as the major Arabidopsis Al tolerance protein, AtALMT1, which encodes an aluminum-activated root malate transporter, may influence both Al tolerance and P acquisition via changes in root system morphology and architecture. However, trans-acting elements such as transcription factors (TFs) may be the best option for pleiotropic control of multiple abiotic stress genes, due to their small and often multiple binding sequences in the genome. One such example is the C2H2-type zinc finger, AtSTOP1, which is a transcriptional regulator of a number of Arabidopsis Al tolerance genes, including AtMATE and AtALMT1, and has been shown to activate AtALMT1, not only in response to Al but also low soil P. The large WRKY family of transcription factors are also known to affect a broad spectrum of phenotypes, some of which are related to acidic soil abiotic stress responses. Hence, we focus here on signaling proteins such as TFs and protein kinases to identify, from the literature, evidence for unifying regulatory networks controlling Al tolerance, P efficiency and, also possibly drought tolerance. Particular emphasis will be given to modification of root system morphology and architecture, which could be an important physiological "hub" leading to crop adaptation to multiple soil-based abiotic stress factors.

Classical and Molecular Approaches for Mapping of Genes and Quantitative Trait Loci in Peanut

Abstract: Advances in availability of genomic resources coupled with genetic resources have accelerated the process of developing better understanding of cytogenetics and genetics of peanut using modern technologies. The cytogenetic studies provided greater insights on chromosomal structures and behaviour of different Arachis species along with their genetic relationship with each other. Researchers are moving faster now in using single nucleotide polymorphism (SNP) markers in their genetic studies as simple sequence repeats (SSRs) did not provide optimum genome density for genetic mapping studies in peanut. Due to availability of reference genome of diploid progenitors, resequencing of some genotypes and soon to be available tetraploid genome, a high-density genotyping array with 58 K SNPs is now available for conducting high-resolution mapping in peanut. ICRISAT has developed next generation genetic mapping populations such as multi-parent advanced generation intercross (MAGIC) and nested association mapping (NAM) populations for conducting high-resolution trait mapping for multiple traits in one go. Affordability of sequencing also encouraged initiation of sequence-based trait mapping such as QTL-seq for dissecting foliar disease resistance trait. Few successful examples are available in peanut regarding development of diagnostic markers and their deployment in breeding to develop improved genotypes, which may see a significant increase in coming years for developing appropriate genomics tools for breeding in peanut.

Genomic selection in animal breeding programs.

Abstract: Genomic selection can have a major impact on animal breeding programs, especially where traits that are important in the breeding objective are hard to select for otherwise. Genomic selection provides more accurate estimates for breeding value earlier in the life of breeding animals, giving more selection accuracy and allowing lower generation intervals. From sheep to dairy cattle, the rates of genetic improvement could increase from 20 to 100 % and hard-to-measure traits can be improved more effectively.Reference populations for genomic selection need to be large, with thousands of animals measured for phenotype and genotype. The smaller the effective size of the breeding population, the larger the DNA segments they potentially share and the more accurate genomic prediction will be. The relative contribution of information from relatives in the reference population will be larger if the baseline accuracy is low, but such information is limited to closely related individuals and does not last over generations.