Linkage and regional association analysis reveal two new tightly-linked major-QTLs for pod number and seed number per pod in rapeseed (Brassica napus L.)

Abstract

To facilitate the pseudochromosomes assembly and gene cloning in rapeseed, we developed a reference genetic population/map (named BnaZNF2) from two sequenced cultivars, Zhongshuang11 and No.73290, those exhibit significant differences in many traits, particularly yield components. The BnaZNF2 genetic map exhibited perfect collinearity with the physical map of B. napus, indicating its high quality. Comparative mapping revealed several genomic rearrangements between B. napus and B. rapa or B. oleracea. A total of eight and 16 QTLs were identified for pod number and seed number per pod, respectively, and of which three and five QTLs are identical to previously identified ones, whereas the other five and 11 are novel. Two new major QTL respectively for pod number and seed number per pod, qPN.A06-1 and qSN.A06-1 (R2 = 22.8% and 32.1%), were colocalised with opposite effects, and only qPN.A06-1 was confirmed and narrowed by regional association analysis to 180 kb including only 33 annotated genes. Conditional QTL analysis and subsequent NILs test indicated that tight linkage, rather than pleiotropy, was the genetic causation of their colocalisation. Our study demonstrates potential of this reference genetic population/map for precise QTL mapping and as a base for positional gene cloning in rapeseed.

An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)

“…Pod number, especially from branch inflorescence and whole plant, is also the most variable among the three yield components, in accordance with its modest heritability observed in most studies [2, 3]. In rapeseed germplasm resources, pod number shows extensive natural variation, which is invaluable for the genetic improvement [4]. However, the genetic and especially the molecular mechanism for this kind of variation are poorly understood.…”

“…To the present, more than 80 pod number quantitative trait loci (QTLs) have been identified from nearly ten linkage mapping populations [4]. However, only a few of these QTLs were repeatedly detected, in accordance with the modest heritability of pod number.…”

“…However, only a few of these QTLs were repeatedly detected, in accordance with the modest heritability of pod number. In addition, almost all of these pod number QTLs showed a moderate effect [4]. Therefore, it is difficult to narrow down these pod number QTLs and identify the underlying candidate genes.…”

“…In our previous study, we screened two rapeseed cultivars Zhongshuang11 and No.73290 that showed significant difference in pod number [4] mainly due to the difference in floral organ number. The main objectives of our study are to: (1) dissect the genetic mechanism of pod number variation by QTL mapping using BnaZNRIL and BnaZNF 2 population derived from Zhongshuang11 and No.73290; (2) dissect the molecular mechanism of pod number variation by characterizing the expression profile and DEGs of SAM for Zhongshuang11 and No.73290 using RNA sequencing technology; (3) integrate the QTLs and DEGs to identify potential candidate genes for further functional and mechanism studies.…”

Phenotyping and genotyping parents of sixteen recombinant inbred peanut populations

“…Previously, the number of seeds per pod was mapped in soybean to a 0.7 cM genomic region containing the Ln-encoding gene (Glyma20g25000.1) which was proposed to be the candidate gene (Jeong et al, 2011;Jeong et al, 2012). Mapping of seeds per pod in rapeseed also led to discovery of a major QTL explaining 32% of phenotypic variation (Shi et al, 2015). Further genetic mapping of seeds per pod in peanut will shed light on the genetic control of this important agronomic trait.…”