AUTHOR=Raman Harsh , Raman Rosy , Sharma Niharika , Cui Xiaobo , McVittie Brett , Qiu Yu , Zhang Yuanyuan , Hu Qiong , Liu Shengyi , Gororo Nelson 

TITLE=Novel quantitative trait loci from an interspecific Brassica rapa derivative improve pod shatter resistance in Brassica napus

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1233996

DOI=10.3389/fpls.2023.1233996

ISSN=1664-462X

ABSTRACT=<p>Pod shatter is a trait of agricultural relevance that ensures plants dehisce seeds in their native environment and has been subjected to domestication and selection for non-shattering types in several broadacre crops. However, pod shattering causes a significant yield reduction in canola (<italic>Brassica napus</italic> L.) crops. An interspecific breeding line BC95042 derived from a <italic>B. rapa/B. napus</italic> cross showed improved pod shatter resistance (up to 12-fold than a shatter-prone <italic>B. napus</italic> variety). To uncover the genetic basis and improve pod shatter resistance in new varieties, we analysed F<sub>2</sub> and F<sub>2:3</sub> derived populations from the cross between BC95042 and an advanced breeding line, BC95041, and genotyped with 15,498 DArTseq markers. Through genome scan, interval and inclusive composite interval mapping analyses, we identified seven quantitative trait loci (QTLs) associated with pod rupture energy, a measure for pod shatter resistance or pod strength, and they locate on A02, A03, A05, A09 and C01 chromosomes. Both parental lines contributed alleles for pod shatter resistance. We identified five pairs of significant epistatic QTLs for additive x additive, additive dominance and dominance x dominance interactions between A01/C01, A03/A07, A07/C03, A03/C03, and C01/C02 chromosomes for rupture energy. QTL effects on A03/A07 and A01/C01 were in the repulsion phase. Comparative mapping identified several candidate genes (<italic>AG</italic>, <italic>ABI3</italic>, <italic>ARF3</italic>, <italic>BP1</italic>, <italic>CEL6</italic>, <italic>FIL, FUL</italic>, <italic>GA2OX2</italic>, <italic>IND</italic>, <italic>LATE</italic>, <italic>LEUNIG</italic>, <italic>MAGL15</italic>, <italic>RPL</italic>, <italic>QRT2</italic>, <italic>RGA</italic>, <italic>SPT</italic> and <italic>TCP10</italic>) underlying main QTL and epistatic QTL interactions for pod shatter resistance. Three QTLs detected on A02, A03, and A09 were near the <italic>FUL (FRUITFULL)</italic> homologues <italic>BnaA03g39820D</italic> and <italic>BnaA09g05500D</italic>. Focusing on the <italic>FUL</italic>, we investigated putative motifs, sequence variants and the evolutionary rate of its homologues in 373 resequenced <italic>B. napus</italic> accessions of interest. <italic>BnaA09g05500D</italic> is subjected to purifying selection as it had a low Ka/Ks ratio compared to other <italic>FUL</italic> homologues in <italic>B. napus.</italic> This study provides a valuable resource for genetic improvement for yield through an understanding of the genetic mechanism controlling pod shatter resistance in <italic>Brassica</italic> species.</p>