Identification and validation of stable and novel quantitative trait loci for pod shattering in soybean[Glycine max(L.)Merr.]

Pod shattering is an important domesticated trait which can cause great economic loss of crop yield in cultivated soybean.In this study,we utilized two recombinant inbred line populations(RILs,CY,Huachun 2×Wayao;GB,Guizao 1×B13)to identify quantitative trait loci(QTLs)associated with pod shattering in soybean across multiple environments.A total of 14 QTLs for pod shattering were identified in the two RIL populations,which had LOD scores ranging from 2.64 to 44.33 with phenotypic variance explanation(PVE)ranging from 1.33 to 50.85%.One QTL qPS16-1,located on chromosome 16,included a well-known functional gene Pod dehiscence 1(Pdh1)that was reported previously.Ten new putative QTLs were validated in two RIL populations,and their LOD scores were between 2.55 and 4.24,explaining 1.33 to 2.60%of the phenotypic variation.Of which four novel QTLs(qPS01-1,qPS03-2,qPS05-1,and qPS07-1)could be detected in two environments where nine genes had specific changes in gene expression.Although the nine genes may have significant effects on pod shattering of soybean,their detailed functions still need to be further explored in the future.The results of this study will facilitate a better understanding of the genetic basis of the pod shattering-resistant trait and benefit soybean molecular breeding for improving pod shattering resistance.

Elimination of an unfavorable allele conferring pod shattering in an elite soybean cultivar by CRISPR/Cas9

Pod shattering can lead to devastating yield loss of soybean and has been a negatively selected trait in soybean domestication and breeding.Nevertheless,a significant portion of soybean cultivars are still pod shattering-susceptible,limiting their regional and climatic adaptabilities.Here we performed genetic diagnosis on the shattering-susceptible trait of a national registered cultivar,Huachun6(HC6),and found that HC6 carries the susceptible genotype of a candidate Pod dehiscence 1(PDH1)gene,which exists in a significant portion of soybean cultivars.We next performed genome editing on PDH1 gene by clustered regularly interspaced short palindromic repeats(CRISPR)-CRISPR-associated protein 9(Cas9).In T2 progenies,several transgene-free lines with pdh1 mutations were characterized without affecting major agronomic traits.The pdh1 mutation significantly improved the pod shattering resistance which is associated with aberrant lignin distribution in inner sclerenchyma.Our work demonstrated that precision breeding by genome editing on PDH1 holds great potential for precisely improving pod shattering resistance and adaptability of soybean cultivars.

A lignified-layer bridge controlled by a single recessive gene is associated with high pod-shatter resistance in Brassica napus L.

Pod shattering causes severe yield loss in rapeseed(Brassica napus L.)under modern agricultural practice.Identification of highly shatter-resistant germplasm is desirable for the development of rapeseed cultivars for mechanical harvesting.In the present study,an elite line OR88 with strong shatter resistance and a lignified-layer bridge(LLB)structure was identified.The LLB structure was unique to OR88 and co-segregated with high pod-shatter resistance.The LLB structure is differentiated at stage 12 of gynoecium development without any gynoecium defects.Genetic analysis showed that LLB is controlled by a single recessive gene.By BSA-Seq and map-based cloning,the resistance gene location was delimited to a0.688 Mb region on chromosome C09.Transcriptome analysis suggested Bn TCP8.C09 as the gene responsible for LLB.The expression of Bn TCP.C09 was strongly downregulated in OR88,suppressing cell proliferation in the pod valve margin.KASP markers linked to the candidate gene were developed.This pod shatter-resistant line could be used in rapeseed breeding programs by direct transfer of the gene with the assistance of the DNA markers.

Combining Ability and Breeding Potential of Rapeseed Elite Lines for Pod Shatter Resistance

Pod shatter resistance of rapeseed is of great importance for modem farming practice. In order to determine the combining ability of elite inbred lines and the breeding potential of rapeseed hybrids in terms of pod shatter resistance, analysis of a 6×6 incomplete diallel cross was conducted at two locations. Results showed that a significant variation existed among breeding lines and their F1 hybrids for pod shatter resistant index （SRI）, pod length and width. Pod shatter resistance was significantly positively correlated with pod length. The general combining ability （GCA） effects （GCA=l.58） played a more important role than specific combining ability （SCA） effects （SCA=0.20） for pod shatter trait. The elite lines R1, 1019B and 1055B displayed significant positive GCA effects for pod shatter resistance. Four crosses （1019B×R1, 1015B×R1, 6098B×R1, and 8908B×R1） with high mean performance and positive SCA effects were recommended for developing new hybrids for mechanical harvest in the middle reaches of the Yangtze River.

The domestication-associated L1 gene encodes a eucomic acid synthase pleiotropically modulating pod pigmentation and shattering in soybean

Pod coloration is a domestication-related trait in soybean,with modern cultivars typically displaying brown or tan pods,while their wild relative,Glycine soja,possesses black pods.However,the factors regulating this color variation remain unknown.In this study,we cloned and characterized L1,the classical locus responsible for black pods in soybean.By using map-based cloning and genetic analyses,we identified the causal gene of L1 and revealed that it encodes a hydroxymethylglutaryl-coenzyme A(CoA)lyase-like(HMGL-like)domain protein.Biochemical assays showed that L1 functions as a eucomic acid synthase and facilitates the synthesis of eucomic acid and piscidic acid,both of which contribute to coloration of pods and seed coats in soybean.Interestingly,we found that L1 plants are more prone to pod shattering under light exposure than l1 null mutants because dark pigmentation increases photothermal efficiency.Hence,pleiotropic effects of L1 on pod color and shattering,as well as seed pigmentation,likely contributed to the preference forl1 alleles during soybean domestication and improvement.Collectively,our study provides new insights into the mechanism of pod coloration and identifies a new target for future de novo domestication oflegume crops.