Multigenic Control of Pod Shattering Resistance in Chinese Rapeseed Germplasm Revealed by Genome-Wide Association and Linkage Analyses

Abstract

The majority of rapeseed cultivars shatter seeds upon maturity especially under hot-dry and windy conditions, reducing yield and gross margin return to growers. Here, we identified quantitative trait loci (QTL) for resistance to pod shatter in an unstructured diverse panel of 143 rapeseed accessions, and two structured populations derived from bi-parental doubled haploid (DH) and inter-mated (IF2) crosses derived from R1 (resistant to pod shattering) and R2 (prone to pod shattering) accessions. Genome-wide association analysis identified six significant QTL for resistance to pod shatter located on chromosomes A01, A06, A07, A09, C02, and C05. Two of the QTL, qSRI.A09 delimited with the SNP marker Bn-A09-p30171993 (A09) and qSRI.A06 delimited with the SNP marker Bn-A06-p115948 (A06) could be repeatedly detected across environments in a diversity panel, DH and IF2 populations, suggesting that at least two loci on chromosomes A06 and A09 were the main contributors to pod shatter resistance in Chinese germplasm. Significant SNP markers identified in this study especially those that appeared repeatedly across environments provide a cost-effective and an efficient method for introgression and pyramiding of favorable alleles for pod shatter resistance via marker-assisted selection in rapeseed improvement programs.

An Epigenetic LTR-retrotransposon insertion in the upstream region ofBnSHP1.A9controls quantitative pod shattering resistance inBrassica napus

“…In addition, we used a total of 135 diverse accessions, comprised of four winter type, 119 semi-winter type and 12 spring type (Supplemental table 1) to validate the association between pod shatter resistance index (PSRI) and the BnSHP1.A9 promoter specific marker. All accessions were evaluated for pod shatter resistance using random impact test as described previously (Liu et al, 2016).…”

“…The 96 DH lines derived from R1/R2 cross were genotyped with an InDel marker BnSHP1.A9-IF4 and other new InDel and SSR makers developed based on sequence variation between the two parental lines in the vicinity of qSRI.A9 region (Supplemental table 2). This polymorphic data was integrated with the Illumina Brassica 60K Infinium ® SNP array and pod shatter resistance data generated in our previous study (Liu et al, 2016). To determine putative QTL for pod shatter resistance, we performed the composite interval mapping (CIM) using WinQTL Cartographer 2.50 (Zeng, 1994; Wang et al, 2006).…”

“…Comparative mapping studies have shown that the SHATTERPROOF paralogs of A. thaliana ( SHP1 and SHP2 ) are located in the vicinity of the QTL associated with pod shatter resistance on chromosome A9 (designated as BnSHP1.A9 and BnSHP2.A9 ) in Australian and Chinese oilseed rape populations, including the R1/R2 DH population utilized in this study (Liu et al, 2016; Raman et al, 2014). SHP1 and SHP2 are MADS-box genes, which regulate cell differentiation of the valve margin and promote lignification (Liljegren et al, 2000).…”

“…Genetic variation for pod shatter resistance exists in Brassica napus , Brassica rapa , Brassica juncea and Brassica carinata germplasm (Hu et al, 2012; Liu et al, 2016; Raman et al, 2014; Raman et al, 2017; Kadkol et al, 1984), and can be exploited to breed commercial varieties with improved pod shatter resistance. Genetic studies have revealed that pod shatter resistance is controlled by multiple genes.…”

“…Genetic studies have revealed that pod shatter resistance is controlled by multiple genes. Several quantitative trait loci (QTL) associated with this trait have been localized on genetic and physical maps of oilseed rape (Hu et al, 2012; Raman et al, 2014; Liu et al, 2016). However, the identification of corresponding genes underlying QTL for pod shatter resistance in B. napus has not been reported yet.…”