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Durability of the resistance to anthracnose, caused by Colletotrichum lindemuthianum (Sacc. & Magnus) Lambs.‐Scrib., could be increased if more than one resistance gene were incorporated into current bean (Phaseolus vulgaris L.) cultivars. The objective of this study was to identify random amplified polymorphic DNA (RAPD) markers linked to three independent resistance loci to facilitate gene pyramiding in common bean. Markers were identified by means of bulked segregant analysis and heterogeneous inbred populations. RAPD marker OF10530 cosegregated in repulsion‐phase (1.9 ± 1.4 cM) with the Co‐1 (A) allele. A survey of diverse bean genotypes showed that the OF10530 RAPD band could facilitate introgression of the Co‐1 gene across the Andean and Middle American Phaseolus gene pools. RAPD marker OAB3450 was linked in coupling‐phase (5.9 ± 1.7 cM) to the Co‐5 (Mexique 3) allele. A coupling‐phase (OAH1780) and repulsion‐phase (OAK20890) RAPD marker were linked to the Co‐6 locus. These markers flanked the Co‐6 locus and mapped at 12.3 ± 1.9 from the Co‐6 allele and at 7.3 ± 1.5 cM from the co‐6 allele, respectively. Coupling and repulsion‐phase RAPD markers used as a codominant pair showed a higher selection efficiency (95%), for the identification of homozygous (Co‐6 Co‐6) F2 individuals, than individual selection either for a coupling‐phase (33%) or against a repulsion‐phase (92%) RAPD phenotype. Durability of resistance to anthracnose could be improved if (i) two major resistance genes were pyramided by marker assisted selection, (ii) different genes were deployed in different regions, and (iii) resistance genes from different gene pools were combined.

Incorporation of the dominant gene Are, of Middle American origin, into commercial cultivars of Phaseolus vulgaris L., has been the main disease control strategy of plant breeders to limit the potential damage of Colletotrichum lindemuthianum (Sacc. & Magnus.) Lams.-Scrib. A random amplified polymorphic DNA (RAPD) marker designated OQ4 1440 , generated by a 5'-AGTGCGCTGA-3' decamer primer, was found tightly linked in coupling with the Are gene. OQ4 1440 mapped at 2.0 ± 1.4 centimorgans (cM) from the Are allele in the Andean genetic background and at 5.5 ± 2.3 CM in the Middle American background. A second coupling phase RAPD marker B355 1000 , generated by the 5'-GTATGGGGCT 3' primer mapped at 5.4 ± 2.3 cM from the Are allele in the Andean genetic background and at 7.7 ± 2.7 CM in the Middle American background. Based on a recombination distance of 7.0 ± 1.9 cM between the two markers, OQ4 1440 and B355 1000 RAPDs appear to flank the Are gene. The bracketing molecular markers allowed tagging of the Are allele with a selection fidelity of 99%. Use of the OQ4 1440 and B355 1000 RAPD markers for marker-based selection will afford the opportunity to retain the Are anthracnose resistance gene in bean germplasm, as other epistatic resistance genes are characterized, and incorporated into contemporary bean cultivars.

Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple.