| Peanut (Arachis hypogaea L.) is one of the important oilseed, cash and edible crops in the world, belonging to one of only two allotetraploid (2n=4x=40) of genus Arachis. Peanut is widely planted in over 100 countries of the world, with the total production of 38,345.5 kt from the annual average planting area of 23,883.7 kha. China is the largest country in peanut production, consumption and trade. Late leaf spot (LLS) caused by Phaeoisariopsis personata van Arx is one of the most destructive foliar diseases of peanut worldwide. Epidemics of LLS are affected by difference of regions and seasons. LLS is the most important peanut desease in the basin of Sichuan. Breeding and application of resistant peanut cultivars is the most effective approach to control the disease. However, the genetic mechanism of resistance to LLS is complex, which involve in initial infection, spot size, conidium and defoliation etc. Resistance to LLS in cultivated peanut is linked with poor traits such as late mature, small seeds and low yield, which has impeded the genetic enhancement for high yield cultivars with resistance. In order to investigate the genetic machanism and characteristics of resistance to LLS, a highly susceptible cultivar Zhonghua 5 and a highly resistant cultivar ICGV86699 were used as parents to build recombined inbred lines population (XA-RILs). The genetic characteristics of resistance to LLS in peanut were studied based on the segregation analysis using genetic models of quantitative traits. SSR markers tested in the XA-RILs were used to construct a genetic linkage map, and QTLs for resistance to LLS were identified in the map. The transcritome and digtal gene expression of the two descendant lines with extremely resistant or susceptible to LLS were studied by RNA-Seq in order to provide theoretical and germplasm basis to LLS resistance breeding.1. The genetic effects of resistance to LLS of XA-RILs were analysed by mixed model for major gene and polygene. The results showed that the LLS resistance among XA-RILs is significantly different and the resistance was controlled by two additive-epistatic major genes and additive-epistatic polygenes. The heritabilities of main genes were 60.10%-86.61% while the heritabilities of polygenes were 6.65%-32.77%.2. The correlation analysis verified that resistance to LLS was linked with some poor agronomic traits such as late maturity, low yield and small seeds. From XA-RILs, an elite line, XA006, was selected as a breeding line possessing high yield and resistance to LLS with other desirable agronomical traits.3. A total of 2623 pairs SSR primers were screened against the parents of XA-RILs. A total of 250 pairs SSR primers were detected the polymorphism between the parents. Out of the 250 markers generated a total of 257 genetic polymorphism loci and were selected to analysize XA-RIL population. A genetic linkage map was constructed, consisting of 157 loci onto 20 linkage groups and covering a total of 789.506 cM with an average distance of 5.763 cM between adjacent loci and 2-40 markers or loci in every linkage groups. Compared with peanut genetic map of integrated consensus, there were 68 common markers or loci in XA-RIL map and consensus map. These markers or loci were distributed in 18 linkage groups of XA-RIL linkage map and 20 linkage groups of consensus map, with consisting of 9 markers consistent with A10 or B10, A02 or B02 into Lg 9 and Lg 2 linkage group, respectively.4. The genotyping and phenotyping data of resistance to LLS in 2011-2013 were analyzed using MCIM method and a total of 11,14 and 11 loci were delected respectively. Among the QTLs, QTLLLS3-10 was detected in three years and generally showed the additive-additive-epistasis effect or additive effect, with effective value between 0.2623-0.5351 and its heritability was between 1.98% and 8.51%. QTLLLS 1-19 were detected in two years (2012-2013) and showed the additive effect and additive-additive-epistasis effect, with effective value between 0.2381 and 0.4699 and its heritability was between 1.74% and 4.94%.5. The result of RNAseq showed that 98916046 clean reads with sequence length 9.9G were obtained using Illumina HiSeqTM 2000, and were assembled into 142300 transcripts consisting of 45130 unigenes with 200-500 bp,29054 unigenes with 500 bp-1 kbp,39590 with 1-2 kbp and 28526 unigenes with more than 2 kbp. The function of a total of 52566 unigenes was annotated based on the following databases:26608 (50.61%) unigenes to Nr,17834(33.92%) unugenes to Nt,7481(14.23%) unigenes to KEGG, 19127(36.38%) unigenes to Swiss-Prot,18940(36.03%) unigenes to Pfam,20778 (39.52%) unigenes to GO,9837(18.71%) unigenes to KOG,3652(7.52%) unigenes to all databases, and while 29176(55.50%) unigenes to only one database.6. The result of DGE analysis showed that:1) 10093899-12912683 clean reads with sequence length 0.50-0.65 G were obtained from digital gene expression libraries of XA1378C, XA1374I, XA1378I, XA1448C, XA1444I and XA1448I; 2) 8467405 10905420 clean reads were aligned to the reference transcriptome databases; 3) 15.65%-17.73% of the total of clean reads with FPKM value over 15 was high expression reads; 4) there were 28409 common expression unigenes with FPKM>0.3 and 112-1744 special expression unigenes among six digital gene expression libraries; 6) 15589 difference expression genes of XA14441 were maximum and 5161 difference expression genes of XA1378C were least. GO enrichment analysis showed that difference expression genes were mainly enriched in GO terms of metabolic process, cellular process, organic substance metabolic process, primary metabolic process, cellular metabolic process of the biological process and catalytic activity of molecular function, and so on. KEGG enrichment analysis showed that difference expression gene were enriched in photosynthesis, photosynthesis-antenna proteins, metabolic pathways, plant hormone signal transduction and ribosome Pathway etc. |
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