Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.).
BACKGROUND
Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding.


RESULTS
SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. 'SNP_only' markers accounted for 89.25% of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9%, and their LOD scores varied from 3.22 to 4.04.


CONCLUSIONS
High-density genetic maps for walnut containing 16 LGs were constructed using the SLAF-seq method with an F1 population. One QTL for walnut anthracnose resistance was identified based on the map. The results will aid molecular marker-assisted breeding and walnut resistance genes identification.
College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China. zhuyufeng20087289@163.com.
Yufeng
Y
Zhu
College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China. yinyanfei111@163.com.
Yanfei
Y
Yin
College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China. yangwere@126.com.
Keqiang
K
Yang
College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China. jhli4856@163.com.
Jihong
J
Li
College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China. syl_1205@126.com.
Yalin
Y
Sang
Biomarker Technologies Corporation, Beijing, P. R. China. huangl@biomarker.com.cn.
Long
L
Huang
Biomarker Technologies Corporation, Beijing, P. R. China. fans@biomarker.com.cn.
Shu
S
Fan
D054458:Amplified Fragment Length Polymorphism Analysis / Q000379:methods*; D002681:China; D002874:Chromosome Mapping / Q000379:methods*; D060467:Disease Resistance; D017343:Genes, Plant; D031324:Juglans / Q000235:genetics* / Q000254:growth & development; D010641:Phenotype; D000069600:Plant Breeding; D040641:Quantitative Trait Loci